AMBER Archive (2009) - By Thread

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Starting: Thu Jan 01 2009 - 21:37:45 CST
Ending: Thu Dec 31 2009 - 22:57:46 CST

AMBER: energy jumps during molecule minimization Paul Ledbetter (Thu Jan 01 2009 - 21:33:30 CST)
- Re: AMBER: energy jumps during molecule minimization David A. Case (Fri Jan 02 2009 - 06:48:23 CST)
Re: AMBER: SMD-related questions Gustavo Seabra (Fri Jan 02 2009 - 07:21:53 CST)
Re: AMBER: RMS plot Carlos Simmerling (Fri Jan 02 2009 - 08:08:44 CST)
- RE: AMBER: RMS plot Duggan, Brendan M. (Tue Jan 06 2009 - 13:54:04 CST)
  - Re: AMBER: RMS plot Carlos Simmerling (Tue Jan 06 2009 - 13:57:50 CST)
Re: AMBER: a question about ff03ua oguz gurbulak (Fri Jan 02 2009 - 09:30:46 CST)
- Re: AMBER: a question about ff03ua David A. Case (Fri Jan 02 2009 - 10:35:15 CST)
- Re: AMBER: a question about ff03ua FyD (Fri Jan 02 2009 - 14:20:37 CST)
AMBER: apparent error in closest function in ptraj 10 Roman Osman (Fri Jan 02 2009 - 09:54:48 CST)
- Re: AMBER: apparent error in closest function in ptraj 10 D.J. Cole (Fri Jan 02 2009 - 10:06:01 CST)
  - Re: AMBER: apparent error in closest function in ptraj 10 Roman Osman (Fri Jan 02 2009 - 11:37:09 CST)
AMBER: Dielectric constant musa özboyacý (Sat Jan 03 2009 - 12:54:06 CST)
AMBER: IMPORTANT INFORMATION: Notice regarding transition of AMBER mailing list to new address. Ross Walker (Sat Jan 03 2009 - 16:12:19 CST)
AMBER: CHCl3 solvent box WJ Ding (Sun Jan 04 2009 - 16:24:48 CST)
- Re: AMBER: CHCl3 solvent box David A. Case (Mon Jan 05 2009 - 07:48:44 CST)
  - Re: AMBER: CHCl3 solvent box WJ Ding (Mon Jan 05 2009 - 15:21:32 CST)
AMBER: reg sander crashing on more than 32 cores over IB Amit Bajaj (Mon Jan 05 2009 - 00:33:15 CST)
- Re: AMBER: reg sander crashing on more than 32 cores over IB David A. Case (Mon Jan 05 2009 - 06:47:01 CST)
AMBER: bug of the mm_pbsa module in ambertools 1.2 Ye Mei (Mon Jan 05 2009 - 09:28:02 CST)
- Re: AMBER: bug of the mm_pbsa module in ambertools 1.2 Scott Brozell (Tue Jan 06 2009 - 12:59:15 CST)
AMBER: ligand parameter Bo Baker (Mon Jan 05 2009 - 16:05:18 CST)
- RE: AMBER: ligand parameter Ross Walker (Mon Jan 05 2009 - 23:48:13 CST)
  - [AMBER] Re: AMBER: ligand parameter Bo Baker (Tue Jan 06 2009 - 21:59:19 CST)
AMBER: error in amber 10 archana sonawani (Tue Jan 06 2009 - 01:19:03 CST)
- Re: AMBER: error in amber 10 David A. Case (Tue Jan 06 2009 - 06:18:23 CST)
  - Re: AMBER: error in amber 10 David A. Case (Tue Jan 06 2009 - 06:28:54 CST)
AMBER: questions about equilibram wei zhang (Tue Jan 06 2009 - 05:18:47 CST)
- [AMBER] Re: AMBER: questions about equilibram David A. Case (Wed Jan 07 2009 - 06:54:10 CST)
  - RE: [AMBER] Re: AMBER: questions about equilibram wei zhang (Tue Jan 13 2009 - 06:58:51 CST)
AMBER: Re: nmode error: bad nonbon (amber 10) Jeremy Harris (Tue Jan 06 2009 - 07:37:21 CST)
- Re: AMBER: Re: nmode error: bad nonbon (amber 10) David A. Case (Tue Jan 06 2009 - 08:32:48 CST)
  - [AMBER] Re: AMBER: Re: nmode error: bad nonbon (amber 10) Jeremy Harris (Tue Jan 13 2009 - 15:58:36 CST)
    - Re: [AMBER] Re: AMBER: Re: nmode error: bad nonbon (amber 10) David A. Case (Wed Jan 14 2009 - 07:13:18 CST)
AMBER: install amber10 wl2290_at_columbia.edu (Tue Jan 06 2009 - 11:23:01 CST)
- Re: AMBER: install amber10 Scott Brozell (Tue Jan 06 2009 - 13:33:21 CST)
AMBER: problem with ptraj image command in Amber 10? Ryan Pavlovicz (Tue Jan 06 2009 - 11:28:27 CST)
- Re: AMBER: problem with ptraj image command in Amber 10? Carlos Simmerling (Tue Jan 06 2009 - 11:37:51 CST)
AMBER: xleap problem Bala subramanian (Tue Jan 06 2009 - 12:57:53 CST)
- Re: AMBER: xleap problem Carlos Simmerling (Tue Jan 06 2009 - 13:05:31 CST)
  - Re: AMBER: xleap problem Bala subramanian (Tue Jan 06 2009 - 13:43:00 CST)
Re: AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) Scott Brozell (Tue Jan 06 2009 - 13:23:29 CST)
AMBER: IMPORTANT Information regarding AMBER Mailing List - please read. Ross Walker (Tue Jan 06 2009 - 14:40:00 CST)
AMBER: mail list Mark M Huntress (Tue Jan 06 2009 - 17:06:57 CST)
- [AMBER] RE: AMBER: mail list Ross Walker (Tue Jan 06 2009 - 17:47:08 CST)
  - Re: [AMBER] RE: AMBER: mail list James W. Caldwell (Tue Jan 06 2009 - 19:24:12 CST)
  - Re: [AMBER] RE: AMBER: mail list M. L. Dodson (Wed Jan 07 2009 - 10:04:02 CST)
[AMBER] amber@ambermd.org open for business Ross Walker (Tue Jan 06 2009 - 17:34:31 CST)
AMBER: REMINDER: The amber@scripps.edu mailing list is now CLOSED Ross Walker (Tue Jan 06 2009 - 17:40:50 CST)
[AMBER] TEST Message - please ignore. Ross Walker (Tue Jan 06 2009 - 19:00:39 CST)
[AMBER] AMBER: Problems in solvation with xleap vallespardojl_at_chem.leidenuniv.nl (Wed Jan 07 2009 - 07:39:56 CST)
[AMBER] MD Beale, John (Wed Jan 07 2009 - 08:40:07 CST)
- RE: [AMBER] MD Ross Walker (Wed Jan 07 2009 - 18:33:46 CST)
[AMBER] four prepin/frcmod files be read simultaneously by leap Yi Mao (Wed Jan 07 2009 - 08:46:05 CST)
- Re: [AMBER] four prepin/frcmod files be read simultaneously by leap rpaduri_at_chem.wayne.edu (Wed Jan 07 2009 - 10:05:09 CST)
  - Re: [AMBER] four prepin/frcmod files be read simultaneously by leap Yi Mao (Wed Jan 07 2009 - 10:38:52 CST)
    - Re: [AMBER] four prepin/frcmod files be read simultaneously by leap David A. Case (Wed Jan 07 2009 - 12:39:56 CST)
[AMBER] PBSA: PB bomb in pb_setgrd() Larry Layne (Wed Jan 07 2009 - 09:33:57 CST)
- RE: [AMBER] PBSA: PB bomb in pb_setgrd() Ray Luo (Wed Jan 07 2009 - 12:24:15 CST)
[AMBER] RE: RE: amber force filed for RNA Ross Walker (Wed Jan 07 2009 - 10:49:41 CST)
[AMBER] RE: same result Ross Walker (Wed Jan 07 2009 - 10:59:39 CST)
- Re: [AMBER] RE: same result zgong.hust (Thu Jan 08 2009 - 02:49:29 CST)
[AMBER] Amber Parameters for Iron Heme covalently boud to carbon monoxide Osmar Norberto de Souza (Wed Jan 07 2009 - 12:23:06 CST)
[AMBER] PHOSPHOTHREONINE Khaled Barakat (Wed Jan 07 2009 - 13:11:43 CST)
- Re: [AMBER] PHOSPHOTHREONINE David A. Case (Wed Jan 07 2009 - 13:29:35 CST)
[AMBER] Using GAFF with a covalently bound ligand or label Sale, Kenneth L (Wed Jan 07 2009 - 19:30:10 CST)
- Re: [AMBER] Using GAFF with a covalently bound ligand or label David A. Case (Wed Jan 07 2009 - 20:42:27 CST)
- Re: [AMBER] Using GAFF with a covalently bound ligand or label Markus Kaukonen (Fri Jan 16 2009 - 00:31:53 CST)
  - Re: [AMBER] Using GAFF with a covalently bound ligand or label FyD (Fri Jan 16 2009 - 03:13:43 CST)
[AMBER] Non-planarity of amide atoms after optimization Sanghwa Han (Wed Jan 07 2009 - 21:17:18 CST)
[AMBER] how many processors for parallel test michael (Thu Jan 08 2009 - 05:01:41 CST)
- Re: [AMBER] how many processors for parallel test David A. Case (Thu Jan 08 2009 - 06:08:06 CST)
  - Re: [AMBER] how many processors for parallel test michael bane (Thu Jan 08 2009 - 07:31:31 CST)
    - Re: [AMBER] how many processors for parallel test David A. Case (Thu Jan 08 2009 - 07:44:52 CST)
    - Re: [AMBER] how many processors for parallel test michael bane (Thu Jan 08 2009 - 07:56:59 CST)
[AMBER] Can we use Amber? Casey,Richard (Thu Jan 08 2009 - 11:16:50 CST)
[AMBER] mairun wl2290_at_columbia.edu (Thu Jan 08 2009 - 11:30:05 CST)
- RE: [AMBER] mairun Ross Walker (Thu Jan 08 2009 - 12:25:26 CST)
  - RE: [AMBER] mairun wl2290_at_columbia.edu (Thu Jan 08 2009 - 16:33:52 CST)
    - RE: [AMBER] mairun Ross Walker (Thu Jan 08 2009 - 16:51:49 CST)
    - RE: [AMBER] mairun wl2290_at_columbia.edu (Thu Jan 08 2009 - 17:11:56 CST)
[AMBER] Can we use AMBER? Casey,Richard (Thu Jan 08 2009 - 11:25:57 CST)
- RE: [AMBER] Can we use AMBER? Ross Walker (Thu Jan 08 2009 - 12:47:18 CST)
[AMBER] lone pairs on CYX and MET Beale, John (Thu Jan 08 2009 - 12:08:42 CST)
- RE: [AMBER] lone pairs on CYX and MET Ross Walker (Thu Jan 08 2009 - 12:17:52 CST)
[AMBER] Need help with point to plane distance calculation in nab M. L. Dodson (Thu Jan 08 2009 - 12:39:16 CST)
- Re: [AMBER] Need help with point to plane distance calculation in nab IN SUK JOUNG (Thu Jan 08 2009 - 13:00:20 CST)
  - Re: [AMBER] Need help with point to plane distance calculation in nab M. L. Dodson (Thu Jan 08 2009 - 13:16:51 CST)
    - Re: [AMBER] Need help with point to plane distance calculation in nab IN SUK JOUNG (Thu Jan 08 2009 - 13:41:09 CST)
    - Re: [AMBER] Need help with point to plane distance calculation in nab M. L. Dodson (Thu Jan 08 2009 - 13:54:15 CST)
RE: [AMBER] mpirun Ross Walker (Thu Jan 08 2009 - 17:28:12 CST)
[AMBER] force-field for cyclic oligosaccharide using leap Madhurima Jana (Thu Jan 08 2009 - 22:50:18 CST)
- [AMBER] force-field for cyclic oligosaccharide using leap Madhurima Jana (Sun Jan 11 2009 - 22:21:23 CST)
[AMBER] NAB entropy calcualtion chaitanya koppisetty (Fri Jan 09 2009 - 03:01:13 CST)
- Re: [AMBER] NAB entropy calcualtion Andreas Svrcek-Seiler (Fri Jan 09 2009 - 03:28:48 CST)
- Re: [AMBER] NAB entropy calcualtion David A. Case (Fri Jan 09 2009 - 07:13:32 CST)
[AMBER] ambpdb is changing atom names, a feature or bug? Markus Kaukonen (Fri Jan 09 2009 - 06:55:41 CST)
- Re: [AMBER] ambpdb is changing atom names, a feature or bug? David A. Case (Fri Jan 09 2009 - 07:01:54 CST)
[AMBER] problem building AmberTools/sleap on AIX Shan-ho Tsai (Fri Jan 09 2009 - 10:27:56 CST)
- Re: [AMBER] problem building AmberTools/sleap on AIX Wei Zhang (Fri Jan 09 2009 - 10:37:43 CST)
  - Re: [AMBER] problem building AmberTools/sleap on AIX Shan-ho Tsai (Fri Jan 09 2009 - 10:46:59 CST)
- Re: [AMBER] problem building AmberTools/sleap on AIX Bill Ross (Fri Jan 09 2009 - 11:45:55 CST)
  - Re: [AMBER] problem building AmberTools/sleap on AIX Shan-ho Tsai (Fri Jan 09 2009 - 15:49:17 CST)
[AMBER] "bad atom type" Akansha Saxena (Fri Jan 09 2009 - 11:15:11 CST)
Re: [AMBER] ambpdb is changing atom names, a feature or bug? Bill Ross (Fri Jan 09 2009 - 11:53:23 CST)
- Re: [AMBER] ambpdb is changing atom names, a feature or bug? David A. Case (Fri Jan 09 2009 - 12:58:20 CST)
- Re: Re: [AMBER] ambpdb is changing atom names, a feature or bug? Ye Mei (Sat Jan 10 2009 - 02:03:10 CST)
  - Re: Re: [AMBER] ambpdb is changing atom names, a feature or bug? David A. Case (Sat Jan 10 2009 - 10:02:53 CST)
[AMBER] number-of-EPS-exceeds-MAXESP Karol Kaszuba (Fri Jan 09 2009 - 15:07:13 CST)
- Re: [AMBER] number-of-EPS-exceeds-MAXESP FyD (Sat Jan 10 2009 - 02:26:13 CST)
  - Re: [AMBER] number-of-EPS-exceeds-MAXESP Karol Kaszuba (Sat Jan 10 2009 - 09:27:08 CST)
    - Re: [AMBER] number-of-EPS-exceeds-MAXESP FyD (Sun Jan 11 2009 - 01:00:40 CST)
    - Re: [AMBER] number-of-EPS-exceeds-MAXESP Karol Kaszuba (Sun Jan 11 2009 - 02:01:07 CST)
- Re: [AMBER] number-of-EPS-exceeds-MAXESP FyD (Mon Jan 12 2009 - 01:43:48 CST)
  - Re: [AMBER] number-of-EPS-exceeds-MAXESP Karol Kaszuba (Mon Jan 12 2009 - 01:57:50 CST)
    - Re: [AMBER] number-of-EPS-exceeds-MAXESP Karol Kaszuba (Sat Jan 17 2009 - 04:41:22 CST)
[AMBER] implicit and explicit simulation: salt effect Catein Catherine (Fri Jan 09 2009 - 21:03:35 CST)
- Re: [AMBER] implicit and explicit simulation: salt effect David Watson (Fri Jan 09 2009 - 21:49:48 CST)
  - Re: [AMBER] implicit and explicit simulation: salt effect David LeBard (Fri Jan 09 2009 - 22:23:24 CST)
    - Re: [AMBER] implicit and explicit simulation: salt effect David A. Case (Sat Jan 10 2009 - 10:26:45 CST)
- Re: [AMBER] implicit and explicit simulation: salt effect David A. Case (Sat Jan 10 2009 - 10:23:08 CST)
[AMBER] mm-GBSA from implicit Catein Catherine (Fri Jan 09 2009 - 21:13:28 CST)
- Re: [AMBER] mm-GBSA from implicit Carlos Simmerling (Sat Jan 10 2009 - 07:25:10 CST)
[AMBER] Off topic. Hardware problem Francesco Pietra (Sat Jan 10 2009 - 02:26:55 CST)
[AMBER] Can't reproduce RESP charges Sanghwa Han (Sun Jan 11 2009 - 23:57:15 CST)
- Re: [AMBER] Can't reproduce RESP charges FyD (Tue Jan 13 2009 - 05:52:13 CST)
[AMBER] Amber 9 installation problem on Ubuntu drugdesign (Mon Jan 12 2009 - 00:26:34 CST)
- Re: [AMBER] Amber 9 installation problem on Ubuntu David A. Case (Mon Jan 12 2009 - 06:01:31 CST)
[AMBER] Release of the R.E.D.-III.1 tools FyD (Mon Jan 12 2009 - 05:59:14 CST)
[AMBER] Parallelepiped periodic box Ian Streeter (Mon Jan 12 2009 - 09:57:55 CST)
- Re: [AMBER] Parallelepiped periodic box David A. Case (Fri Jan 16 2009 - 13:50:32 CST)
[AMBER] Writing out trajectory in NAB xxxzzzyyy xxxzzzyyy (Mon Jan 12 2009 - 10:43:33 CST)
- Re: [AMBER] Writing out trajectory in NAB David A. Case (Mon Jan 12 2009 - 11:22:58 CST)
[AMBER] crystal waters Carmen Domene (Mon Jan 12 2009 - 14:04:24 CST)
- Re: [AMBER] crystal waters steinbrt_at_rci.rutgers.edu (Mon Jan 12 2009 - 14:16:25 CST)
  - Re: [AMBER] crystal waters Carmen Domene (Mon Jan 12 2009 - 14:32:28 CST)
    - Re: [AMBER] crystal waters steinbrt_at_rci.rutgers.edu (Mon Jan 12 2009 - 14:37:34 CST)
[AMBER] multisander error Justine Condo (Mon Jan 12 2009 - 16:03:37 CST)
- Re: [AMBER] multisander error David Watson (Mon Jan 12 2009 - 16:15:26 CST)
- RE: [AMBER] multisander error Ross Walker (Mon Jan 12 2009 - 16:20:06 CST)
  - Re: [AMBER] multisander error Justine Condo (Mon Jan 12 2009 - 16:32:31 CST)
  - Re: [AMBER] multisander error Justine Condo (Mon Jan 12 2009 - 16:39:44 CST)
    - RE: [AMBER] multisander error Ross Walker (Mon Jan 12 2009 - 16:51:48 CST)
    - Re: [AMBER] multisander error Justine Condo (Mon Jan 12 2009 - 17:01:41 CST)
[AMBER] error in sander (Amber10) archana sonawani (Tue Jan 13 2009 - 02:21:09 CST)
[AMBER] errorin sander---Amber10 archana sonawani (Tue Jan 13 2009 - 03:27:43 CST)
- Re: [AMBER] errorin sander---Amber10 David A. Case (Tue Jan 13 2009 - 07:22:36 CST)
[AMBER] amber9 in fedora10 Bala subramanian (Tue Jan 13 2009 - 11:51:49 CST)
- Re: [AMBER] amber9 in fedora10 Mark Williamson (Tue Jan 13 2009 - 11:56:31 CST)
- RE: [AMBER] amber9 in fedora10 Ross Walker (Tue Jan 13 2009 - 12:00:33 CST)
  - Re: [AMBER] amber9 in fedora10 Bala subramanian (Tue Jan 13 2009 - 12:16:19 CST)
    - Re: [AMBER] amber9 in fedora10 Eric (Tue Jan 13 2009 - 12:28:33 CST)
  - [AMBER] PTRAJ: solvent accessible surface area Catein Catherine (Wed Jan 14 2009 - 01:32:15 CST)
    - Re: [AMBER] PTRAJ: solvent accessible surface area steinbrt_at_rci.rutgers.edu (Wed Jan 14 2009 - 08:59:19 CST)
    - Re: [AMBER] PTRAJ: solvent accessible surface area Carlos Simmerling (Wed Jan 14 2009 - 09:00:59 CST)
[AMBER] principal component vector onto C-alpha Carra, Claudio (JSC-SK)[USRA] (Tue Jan 13 2009 - 14:52:31 CST)
- Re: [AMBER] principal component vector onto C-alpha S.Sundar Raman (Tue Jan 13 2009 - 16:46:20 CST)
[AMBER] Divcon or Mopac Cen Gao (Tue Jan 13 2009 - 17:54:33 CST)
- Re: [AMBER] Divcon or Mopac Martin Peters (Wed Jan 14 2009 - 03:01:12 CST)
[AMBER] ptraj, CHARMM PSF and CMAP Hannes Loeffler (Wed Jan 14 2009 - 03:45:07 CST)
- RE: [AMBER] ptraj, CHARMM PSF and CMAP Ross Walker (Wed Jan 14 2009 - 10:46:17 CST)
[AMBER] charges in topology file vallespardojl_at_chem.leidenuniv.nl (Wed Jan 14 2009 - 04:33:35 CST)
- Re: [AMBER] charges in topology file Carlos Simmerling (Wed Jan 14 2009 - 05:24:52 CST)
- Re: [AMBER] charges in topology file Jeffrey (Fri Jul 10 2009 - 11:20:01 CDT)
[AMBER] reaction coordinates Rausch, Felix (Wed Jan 14 2009 - 05:54:57 CST)
- Re: [AMBER] reaction coordinates David A. Case (Wed Jan 14 2009 - 07:00:59 CST)
  - RE: [AMBER] reaction coordinates Catein Catherine (Wed Jan 14 2009 - 23:25:31 CST)
[AMBER] antechamber cation failure Rausch, Felix (Wed Jan 14 2009 - 07:32:04 CST)
- RE: [AMBER] antechamber cation failure Ross Walker (Wed Jan 14 2009 - 11:45:43 CST)
[AMBER] NPT md with PME method for a water box Jeffrey (Wed Jan 14 2009 - 08:41:24 CST)
- RE: [AMBER] NPT md with PME method for a water box Ross Walker (Wed Jan 14 2009 - 12:07:13 CST)
[AMBER] molecular mechanic minimisation with amber momo momo (Wed Jan 14 2009 - 08:58:47 CST)
- RE: [AMBER] molecular mechanic minimisation with amber Ross Walker (Wed Jan 14 2009 - 11:56:23 CST)
[AMBER] Dipole command in ptraj musa özboyacý (Wed Jan 14 2009 - 09:41:07 CST)
[AMBER] pmemd | Compilation problem with ifort and mvapich environment fohm fohm (Wed Jan 14 2009 - 11:23:50 CST)
- RE: [AMBER] pmemd | Compilation problem with ifort and mvapich environment Ross Walker (Wed Jan 14 2009 - 11:53:20 CST)
[AMBER] bad energy??!! momo momo (Wed Jan 14 2009 - 13:19:20 CST)
- RE: [AMBER] bad energy??!! Ross Walker (Wed Jan 14 2009 - 13:40:24 CST)
[AMBER] Postdoc Position Available at SDSC/UCSD Ross Walker (Wed Jan 14 2009 - 14:35:52 CST)
[AMBER] Dipole command in ptraj musa özboyacý (Wed Jan 14 2009 - 17:15:26 CST)
[AMBER] xmgrace and plotting time evolution of a defined variable Naser Alijabbari (Wed Jan 14 2009 - 18:20:31 CST)
- Re: [AMBER] xmgrace and plotting time evolution of a defined variable Mark Williamson (Wed Jan 14 2009 - 18:38:17 CST)
[AMBER] Error in xleap archana sonawani (Thu Jan 15 2009 - 01:39:16 CST)
- RE: [AMBER] Error in xleap Ross Walker (Thu Jan 15 2009 - 10:01:20 CST)
[AMBER] Using a restart file Simone Swift (Thu Jan 15 2009 - 10:40:38 CST)
- Re: [AMBER] Using a restart file Carlos Simmerling (Thu Jan 15 2009 - 10:45:27 CST)
- RE: [AMBER] Using a restart file Ross Walker (Thu Jan 15 2009 - 10:52:44 CST)
[AMBER] Ligand Diffusion Studies? Jason A. Ford-Green (Thu Jan 15 2009 - 11:42:03 CST)
[AMBER] restraint of REMD z g (Thu Jan 15 2009 - 20:51:46 CST)
- Re: [AMBER] restraint of REMD Carlos Simmerling (Fri Jan 16 2009 - 05:57:29 CST)
[AMBER] sander not working archana sonawani (Thu Jan 15 2009 - 23:52:48 CST)
- Re: [AMBER] sander not working David A. Case (Fri Jan 16 2009 - 08:58:50 CST)
- Re: [AMBER] sander not working Carlos Simmerling (Fri Jan 16 2009 - 09:01:34 CST)
[AMBER] nab conjgrad min problem Jeremy Harris (Fri Jan 16 2009 - 09:11:12 CST)
- Re: [AMBER] nab conjgrad min problem David A. Case (Fri Jan 16 2009 - 09:33:01 CST)
  - Re: [AMBER] nab conjgrad min problem Jeremy Harris (Mon Jan 19 2009 - 09:00:30 CST)
[AMBER] RE: Tutorial 5 Ross Walker (Fri Jan 16 2009 - 11:10:51 CST)
- Re: [AMBER] RE: Tutorial 5 George Tzotzos (Fri Jan 16 2009 - 14:31:11 CST)
[AMBER] (no subject) Lake, Thomas (Fri Jan 16 2009 - 11:38:09 CST)
- Re: [AMBER] (no subject) Carlos Simmerling (Fri Jan 16 2009 - 11:43:26 CST)
  - Re: [AMBER] (no subject) Jenny Iskrenova (Fri Jan 16 2009 - 12:42:08 CST)
[AMBER] Heat and Equilibrate Hybrid GB solvent? Jason A. Ford-Green (Fri Jan 16 2009 - 15:14:41 CST)
- Re: [AMBER] Heat and Equilibrate Hybrid GB solvent? Carlos Simmerling (Fri Jan 16 2009 - 15:21:27 CST)
[AMBER] Use of Amber in distributed calculations drugdesign (Sat Jan 17 2009 - 01:33:55 CST)
- Re: [AMBER] Use of Amber in distributed calculations M. L. Dodson (Sat Jan 17 2009 - 07:48:42 CST)
  - Re: [AMBER] Use of Amber in distributed calculations M. L. Dodson (Sat Jan 17 2009 - 08:01:36 CST)
[AMBER] To stop the AMBER's list Furia Gargano (Sat Jan 17 2009 - 11:59:48 CST)
[AMBER] to remove AMBER list Furia Gargano (Sat Jan 17 2009 - 12:02:26 CST)
- RE: [AMBER] to remove AMBER list Ross Walker (Sat Jan 17 2009 - 15:32:19 CST)
[AMBER] AMBER efficiency: Intel vs. AMD Swarup Gupta (Sun Jan 18 2009 - 19:43:32 CST)
- Re: [AMBER] AMBER efficiency: Intel vs. AMD Ye MEI (Sun Jan 18 2009 - 20:20:47 CST)
- RE: [AMBER] AMBER efficiency: Intel vs. AMD Ross Walker (Mon Jan 19 2009 - 09:39:33 CST)
[AMBER] how to set up "Two molecules tied with an Elastic band of 20A in implicit solvent" Jagadeesh, M.N., Ph.D. (Mon Jan 19 2009 - 03:03:39 CST)
- Re: [AMBER] how to set up "Two molecules tied with an Elastic band of 20A in implicit solvent" Carlos Simmerling (Tue Jan 20 2009 - 08:33:55 CST)
[AMBER] RESP charges for Fe in heme Carina Backtorp (Mon Jan 19 2009 - 07:48:11 CST)
[AMBER] Atom types George Tzotzos (Mon Jan 19 2009 - 08:04:09 CST)
- RE: [AMBER] Atom types Ross Walker (Mon Jan 19 2009 - 09:46:10 CST)
- RE: [AMBER] Atom types George Tzotzos (Mon Jan 19 2009 - 12:02:42 CST)
[AMBER] errors on REMD z g (Mon Jan 19 2009 - 20:41:35 CST)
- Re: [AMBER] errors on REMD Carlos Simmerling (Tue Jan 20 2009 - 05:02:06 CST)
  - Re: [AMBER] errors on REMD z g (Tue Jan 20 2009 - 07:39:12 CST)
[AMBER] analysis Adrien Delmont (Tue Jan 20 2009 - 11:03:16 CST)
[AMBER] Problem with entropy calculation of bigger system using NMODE and NAB. Marek Malý (Tue Jan 20 2009 - 12:24:55 CST)
- RE: [AMBER] Problem with entropy calculation of bigger system using NMODE and NAB. Niel Henriksen (Tue Jan 20 2009 - 14:49:38 CST)
- Re: [AMBER] Problem with entropy calculation of bigger system using NMODE and NAB. David A. Case (Tue Jan 20 2009 - 14:53:48 CST)
  - [AMBER] MD vs scattering Chih-Ying Lin (Tue Jan 20 2009 - 15:10:47 CST)
    - RE: [AMBER] MD vs scattering Ross Walker (Tue Jan 20 2009 - 15:18:26 CST)
    - Re: RE: [AMBER] MD vs scattering Chih-Ying Lin (Tue Jan 20 2009 - 15:26:49 CST)
  - Re: [AMBER] Problem with entropy calculation of bigger system using NMODE and NAB. Marek Malý (Tue Jan 20 2009 - 20:48:03 CST)
[AMBER] solvent mixture iccy liu (Tue Jan 20 2009 - 16:08:34 CST)
- Re: [AMBER] solvent mixture Gustavo Seabra (Sat Jan 24 2009 - 20:44:31 CST)
[AMBER] How to calculate cavity volume from MD structures? ben rodriguez (Tue Jan 20 2009 - 16:21:43 CST)
- Re: [AMBER] How to calculate cavity volume from MD structures? Jason A. Ford-Green (Wed Jan 21 2009 - 09:39:57 CST)
[AMBER] prot-DNA simulation deepti nayar (Wed Jan 21 2009 - 05:16:09 CST)
- Re: [AMBER] prot-DNA simulation Thomas Cheatham III (Wed Jan 21 2009 - 15:55:52 CST)
[AMBER] AMBER External keyword Mahmoud A. A. Ibrahim (Wed Jan 21 2009 - 09:59:33 CST)
- Re: [AMBER] AMBER External keyword Gustavo Seabra (Sat Jan 24 2009 - 20:32:10 CST)
[AMBER] how to use those water models off the list in amber? GZ Zhang (Wed Jan 21 2009 - 15:39:50 CST)
- Re: [AMBER] how to use those water models off the list in amber? Lauren Wickstrom (Wed Jan 21 2009 - 17:58:22 CST)
- Re: [AMBER] how to use those water models off the list in amber? David A. Case (Thu Jan 22 2009 - 07:29:41 CST)
  - Re: [AMBER] how to use those water models off the list in amber? GZ Zhang (Thu Jan 22 2009 - 14:47:02 CST)
[AMBER] reg . parallel run balaji nagarajan (Wed Jan 21 2009 - 23:34:03 CST)
- RE: [AMBER] reg . parallel run Ross Walker (Thu Jan 22 2009 - 09:52:55 CST)
[AMBER] (no subject) Lake, Thomas (Thu Jan 22 2009 - 07:43:59 CST)
- [AMBER] restraining atoms neville forlemu (Thu Jan 22 2009 - 08:53:48 CST)
  - Re: [AMBER] restraining atoms Carlos Simmerling (Thu Jan 22 2009 - 08:55:35 CST)
- RE: [AMBER] (no subject) Ross Walker (Thu Jan 22 2009 - 09:46:56 CST)
[AMBER] MM - PBSA problem musa özboyacý (Thu Jan 22 2009 - 11:06:54 CST)
- RE: [AMBER] MM - PBSA problem Ray Luo (Thu Jan 22 2009 - 11:31:53 CST)
  - Re: [AMBER] MM - PBSA problem musa özboyacý (Thu Jan 22 2009 - 13:52:10 CST)
    - Re: [AMBER] MM - PBSA problem Cenk \(Jenk\) Andac (Thu Jan 22 2009 - 16:00:13 CST)
- RE: [AMBER] MM - PBSA problem Niel Henriksen (Thu Jan 22 2009 - 18:52:09 CST)
  - Re: [AMBER] MM - PBSA problem musa özboyacý (Fri Jan 23 2009 - 07:14:05 CST)
[AMBER] non-natural amino acids Arturas Ziemys (Thu Jan 22 2009 - 11:32:11 CST)
- Re: [AMBER] non-natural amino acids FyD (Thu Jan 22 2009 - 17:25:31 CST)
[AMBER] reg.parallel run error balaji nagarajan (Thu Jan 22 2009 - 12:41:25 CST)
- RE: [AMBER] reg.parallel run error Ross Walker (Thu Jan 22 2009 - 14:06:33 CST)
[AMBER] REM_hybrid test fails on AIX Shan-ho Tsai (Thu Jan 22 2009 - 14:28:04 CST)
- Re: [AMBER] REM_hybrid test fails on AIX Shan-ho Tsai (Thu Feb 05 2009 - 10:44:43 CST)
[AMBER] reg.error in parallel run balaji nagarajan (Fri Jan 23 2009 - 04:05:21 CST)
- RE: [AMBER] reg.error in parallel run Ross Walker (Fri Jan 23 2009 - 09:52:20 CST)
[AMBER] charge derivation for ATP molecule using antechamber prachi munjal (Fri Jan 23 2009 - 07:19:27 CST)
- Re: [AMBER] charge derivation for ATP molecule using antechamber David A. Case (Fri Jan 23 2009 - 10:51:49 CST)
[AMBER] RE: errors on remd Ross Walker (Fri Jan 23 2009 - 10:38:06 CST)
Re: [AMBER] "Could not find bond parameter" George Tzotzos (Fri Jan 23 2009 - 12:16:34 CST)
- RE: [AMBER] "Could not find bond parameter" Ross Walker (Fri Jan 23 2009 - 12:29:46 CST)
[AMBER] reg.parallel.run error balaji nagarajan (Fri Jan 23 2009 - 19:59:21 CST)
- RE: [AMBER] reg.parallel.run error Ross Walker (Sat Jan 24 2009 - 00:05:50 CST)
[AMBER] error on open distatance restraint gmail (Fri Jan 23 2009 - 20:58:27 CST)
- Re: [AMBER] error on open distatance restraint David A. Case (Fri Jan 23 2009 - 21:18:17 CST)
  - Re: [AMBER] error on open distatance restraint xiaonan zhang (Sat Jan 24 2009 - 21:56:02 CST)
[AMBER] reg.parallel.run.error balaji nagarajan (Sat Jan 24 2009 - 09:09:49 CST)
[AMBER] Very weird topology problem ranqi zhu (Sat Jan 24 2009 - 15:14:24 CST)
- Re: [AMBER] Very weird topology problem Peter Gannett (Sat Jan 24 2009 - 17:17:26 CST)
[AMBER] AmberTools and ptraj clustering on Mac OS X David Watson (Sat Jan 24 2009 - 15:41:04 CST)
[AMBER] xleap problem oguz gurbulak (Sun Jan 25 2009 - 05:56:12 CST)
- Re: [AMBER] xleap problem David A. Case (Sun Jan 25 2009 - 07:57:41 CST)
  - Re: [AMBER] xleap problem oguz gurbulak (Sun Jan 25 2009 - 10:02:50 CST)
[AMBER] RE:xleap problem oguz gurbulak (Sun Jan 25 2009 - 10:08:26 CST)
[AMBER] xleap problem oguz gurbulak (Sun Jan 25 2009 - 10:27:48 CST)
[AMBER] xleap problem oguz gurbulak (Sun Jan 25 2009 - 10:34:39 CST)
- Re: [AMBER] xleap problem David A. Case (Sun Jan 25 2009 - 17:30:47 CST)
[AMBER] xleap problem oguz gurbulak (Sun Jan 25 2009 - 05:49:28 CST)
[AMBER] deduce correlation from covariance matrix Yi Mao (Sun Jan 25 2009 - 15:01:05 CST)
[AMBER] using binary trajectories from NAMD in PTRAJ karthik s (Mon Jan 26 2009 - 01:11:29 CST)
- RE: [AMBER] using binary trajectories from NAMD in PTRAJ Wei Huang (Mon Jan 26 2009 - 08:41:22 CST)
  - Re: [AMBER] using binary trajectories from NAMD in PTRAJ karthik s (Tue Jan 27 2009 - 00:49:13 CST)
[AMBER] thioglycoside Alexander Schierholt (Mon Jan 26 2009 - 08:46:28 CST)
- Re: [AMBER] thioglycoside FyD (Mon Jan 26 2009 - 09:07:37 CST)
- Re: [AMBER] thioglycoside Lachele Foley (Lists) (Mon Jan 26 2009 - 09:36:26 CST)
Re: [AMBER] Antechamber Connectivity George Tzotzos (Mon Jan 26 2009 - 12:23:58 CST)
- Re: [AMBER] Antechamber Connectivity David Watson (Mon Jan 26 2009 - 13:59:58 CST)
[AMBER] antechamber : missed atoms Khaled Barakat (Mon Jan 26 2009 - 12:54:07 CST)
- Re: [AMBER] antechamber : missed atoms Khaled Barakat (Mon Jan 26 2009 - 13:15:33 CST)
  - Re: [AMBER] antechamber : missed atoms David A. Case (Tue Jan 27 2009 - 09:23:27 CST)
- Re: [AMBER] antechamber : missed atoms Khaled Barakat (Mon Jan 26 2009 - 13:20:52 CST)
  - Re: [AMBER] antechamber : missed atoms Sean Johnston (Mon Jan 26 2009 - 13:40:59 CST)
- Re: [AMBER] antechamber : missed atoms Khaled Barakat (Mon Jan 26 2009 - 14:22:14 CST)
[AMBER] RE:xleap problem oguz gurbulak (Mon Jan 26 2009 - 13:48:11 CST)
- Re: [AMBER] RE:xleap problem M. L. Dodson (Mon Jan 26 2009 - 14:47:26 CST)
  - Re: [AMBER] RE:xleap problem oguz gurbulak (Mon Jan 26 2009 - 15:40:22 CST)
[AMBER] atom types deepti nayar (Tue Jan 27 2009 - 03:47:12 CST)
- Re: [AMBER] atom types David A. Case (Tue Jan 27 2009 - 09:13:30 CST)
[AMBER] reg: targeted molecular dynamics balaji nagarajan (Tue Jan 27 2009 - 07:02:03 CST)
- Re: [AMBER] reg: targeted molecular dynamics Carlos Simmerling (Tue Jan 27 2009 - 07:04:57 CST)
[AMBER] Rosetta Academic Training Workshop Nir London (Tue Jan 27 2009 - 07:07:24 CST)
[AMBER] reg.Targeted molecular dynamics balaji nagarajan (Tue Jan 27 2009 - 07:56:54 CST)
[AMBER] reg.Targeted molecular dynamics balaji nagarajan (Tue Jan 27 2009 - 07:57:01 CST)
- Re: [AMBER] reg.Targeted molecular dynamics Carlos Simmerling (Wed Jan 28 2009 - 12:01:43 CST)
Re: [AMBER] Antechamber ligand prep George Tzotzos (Tue Jan 27 2009 - 08:48:11 CST)
- Re: [AMBER] Antechamber ligand prep David A. Case (Tue Jan 27 2009 - 08:59:47 CST)
  - Re: [AMBER] Antechamber ligand prep George Tzotzos (Tue Jan 27 2009 - 09:24:30 CST)
[AMBER] NOTICE: File size limits on AMBER reflector Ross Walker (Tue Jan 27 2009 - 10:35:50 CST)
[AMBER] distance restraint and SHAKE Michael J Yonkunas (Tue Jan 27 2009 - 11:39:56 CST)
- Re: [AMBER] distance restraint and SHAKE Thomas Cheatham III (Tue Jan 27 2009 - 12:16:30 CST)
Re: [AMBER] Building atom and angle parameters George Tzotzos (Tue Jan 27 2009 - 12:24:52 CST)
[AMBER] topology file for GLY with amino and carboxyl group? Jose Borreguero (Tue Jan 27 2009 - 12:57:45 CST)
- Re: [AMBER] topology file for GLY with amino and carboxyl group? FyD (Tue Jan 27 2009 - 14:02:14 CST)
[AMBER] large resp charges for non-natural amino acid Arturas Ziemys (Tue Jan 27 2009 - 16:40:49 CST)
- Re: [AMBER] large resp charges for non-natural amino acid FyD (Wed Jan 28 2009 - 22:04:11 CST)
  - Re: [AMBER] large resp charges for non-natural amino acid Arturas Ziemys (Thu Jan 29 2009 - 09:10:50 CST)
- Re: [AMBER] large resp charges for non-natural amino acid Arturas Ziemys (Sat Jan 31 2009 - 11:03:09 CST)
- Re: [AMBER] large resp charges for non-natural amino acid Arturas Ziemys (Sat Jan 31 2009 - 11:03:44 CST)
[AMBER] PhD position in Computational Structural Biology at Cambridge, UK Swanand Gore (Wed Jan 28 2009 - 04:31:16 CST)
[AMBER] GAFF conjugated ring system dihedrals Floris Buelens (Wed Jan 28 2009 - 06:04:55 CST)
- Re: [AMBER] GAFF conjugated ring system dihedrals David A. Case (Thu Jan 29 2009 - 12:37:24 CST)
[AMBER] Watercap... some querries Waqas Nasir (Wed Jan 28 2009 - 08:54:00 CST)
- Re: [AMBER] Watercap... some querries David A. Case (Wed Jan 28 2009 - 09:01:46 CST)
  - Re: [AMBER] Watercap... some querries Waqas Nasir (Wed Jan 28 2009 - 09:10:48 CST)
  - Re: [AMBER] Watercap... some querries Robert Duke (Wed Jan 28 2009 - 12:46:02 CST)
[AMBER] generating top file using antechmaber sarvin moghaddam (Wed Jan 28 2009 - 13:49:20 CST)
- Re: [AMBER] generating top file using antechmaber Wei Zhang (Wed Jan 28 2009 - 14:12:20 CST)
  - Re: [AMBER] generating top file using antechmaber sarvin moghaddam (Thu Jan 29 2009 - 09:24:50 CST)
    - Re: [AMBER] generating top file using antechmaber Wei Zhang (Thu Jan 29 2009 - 10:26:22 CST)
- Re: [AMBER] generating top file using antechmaber Wei Zhang (Wed Jan 28 2009 - 14:23:21 CST)
  - Re: [AMBER] generating top file using antechmaber sarvin moghaddam (Wed Jan 28 2009 - 14:33:00 CST)
    - Re: [AMBER] generating top file using antechmaber David A. Case (Thu Jan 29 2009 - 06:51:56 CST)
[AMBER] Compilation and usage of NAB in parallel ? Marek Malý (Wed Jan 28 2009 - 16:25:24 CST)
- Re: [AMBER] Compilation and usage of NAB in parallel ? David A. Case (Thu Jan 29 2009 - 07:22:08 CST)
  - Re: [AMBER] Compilation and usage of NAB in parallel ? Marek Malý (Fri Jan 30 2009 - 08:59:07 CST)
    - Re: [AMBER] Compilation and usage of NAB in parallel ? David A. Case (Fri Jan 30 2009 - 09:51:31 CST)
    - Re: [AMBER] Compilation and usage of NAB in parallel ? Marek Malý (Fri Jan 30 2009 - 10:01:06 CST)
[AMBER] atomic charge m m (Thu Jan 29 2009 - 02:08:47 CST)
- Re: [AMBER] atomic charge Barbault Florent (Thu Jan 29 2009 - 02:24:48 CST)
[AMBER] Problem in pb simulation, PB_Bomb Waqas Nasir (Thu Jan 29 2009 - 03:08:22 CST)
[AMBER] Dr. Ramesh here kureeckal ramesh (Thu Jan 29 2009 - 04:41:10 CST)
- Re: [AMBER] Dr. Ramesh here rpaduri_at_chem.wayne.edu (Thu Jan 29 2009 - 11:22:20 CST)
  - Re: [AMBER] Dr. Ramesh here kureeckal ramesh (Thu Jan 29 2009 - 19:41:17 CST)
  - Re: [AMBER] Dr. Ramesh here kureeckal ramesh (Thu Jan 29 2009 - 21:18:33 CST)
    - Re: [AMBER] Dr. Ramesh here David A. Case (Fri Jan 30 2009 - 10:08:43 CST)
    - Re: [AMBER] Dr. Ramesh here kureeckal ramesh (Mon Feb 02 2009 - 08:22:51 CST)
[AMBER] Atome Type Mahmoud A. A. Ibrahim (Thu Jan 29 2009 - 04:59:42 CST)
- Re: [AMBER] Atome Type David A. Case (Thu Jan 29 2009 - 07:08:09 CST)
[AMBER] Installation error - Amber10 Ananda Rama Krishnan Selvaraj (Thu Jan 29 2009 - 05:47:44 CST)
- Re: [AMBER] Installation error - Amber10 Andreas Svrcek-Seiler (Thu Jan 29 2009 - 05:52:44 CST)
  - Re: [AMBER] Installation error - Amber10 David A. Case (Thu Jan 29 2009 - 12:33:33 CST)
[AMBER] Problem in watercap simulation, PB_Bomb Waqas Nasir (Thu Jan 29 2009 - 08:21:20 CST)
- RE: [AMBER] Problem in watercap simulation, PB_Bomb Ray Luo (Thu Jan 29 2009 - 11:45:33 CST)
[AMBER] Alpha helix plot Beale, John (Thu Jan 29 2009 - 14:10:11 CST)
- Re: [AMBER] Alpha helix plot Carlos Simmerling (Fri Jan 30 2009 - 16:11:10 CST)
[AMBER] failure to run antechamber with amber 10 Francesco Pietra (Thu Jan 29 2009 - 16:29:18 CST)
- Re: [AMBER] failure to run antechamber with amber 10 David A. Case (Thu Jan 29 2009 - 16:45:53 CST)
  - Re: [AMBER] failure to run antechamber with amber 10 Francesco Pietra (Fri Jan 30 2009 - 02:04:33 CST)
- Re: [AMBER] failure to run antechamber with amber 10 George Tzotzos (Thu Jan 29 2009 - 16:48:50 CST)
[AMBER] AmberTools 1.2 James W. Caldwell (Thu Jan 29 2009 - 18:04:36 CST)
- Re: [AMBER] AmberTools 1.2 David A. Case (Fri Jan 30 2009 - 06:04:41 CST)
[AMBER] adding MG2 problem balaji nagarajan (Fri Jan 30 2009 - 03:45:58 CST)
- Re: [AMBER] adding MG2 problem Scott Brozell (Tue Feb 03 2009 - 13:09:32 CST)
  - RE: [AMBER] adding MG2 problem Rausch, Felix (Wed Feb 04 2009 - 07:04:51 CST)
[AMBER] Xleap - solvatebox - counterions Arnaud (Fri Jan 30 2009 - 04:44:58 CST)
- Re: [AMBER] Xleap - solvatebox - counterions David A. Case (Fri Jan 30 2009 - 10:04:23 CST)
  - RE: [AMBER] Xleap - solvatebox - counterions amirhossein taghavi (Sat Jan 31 2009 - 11:34:10 CST)
[AMBER] help momo momo (Fri Jan 30 2009 - 06:35:22 CST)
- RE: [AMBER] help Ross Walker (Fri Jan 30 2009 - 07:42:33 CST)
[AMBER] Amber top file to Charmm top file sarvin moghaddam (Fri Jan 30 2009 - 08:48:44 CST)
[AMBER] REMD fixed atoms Maxime Louet (Fri Jan 30 2009 - 11:26:08 CST)
- Re: [AMBER] REMD fixed atoms Carlos Simmerling (Sun Feb 01 2009 - 12:00:33 CST)
Re: [AMBER] Xleap - solvatebox - counterions Bill Ross (Fri Jan 30 2009 - 12:40:07 CST)
[AMBER] thermo, entropy by quasiharmonic method Carra, Claudio (JSC-SK)[USRA] (Fri Jan 30 2009 - 15:35:37 CST)
- Re: [AMBER] thermo, entropy by quasiharmonic method David A. Case (Fri Jan 30 2009 - 17:40:38 CST)
[AMBER] RE: Tutorial 5 Ross Walker (Fri Jan 30 2009 - 19:32:03 CST)
- Re: [AMBER] RE: Tutorial 5 George Tzotzos (Sun Feb 01 2009 - 15:04:36 CST)
[AMBER] Test run on Solaris 10 X 86 Manikandan Chandrasekaran (Sat Jan 31 2009 - 12:39:14 CST)
- Re: [AMBER] Test run on Solaris 10 X 86 David A. Case (Sat Jan 31 2009 - 20:49:22 CST)
  - [AMBER] Citing AMBER Tools... Aydin, Cihan (Sat Jan 31 2009 - 23:08:36 CST)
    - Re: [AMBER] Citing AMBER Tools... David A. Case (Thu Feb 05 2009 - 09:44:37 CST)
- Re: [AMBER] Test run on Solaris 10 X 86 Atro Tossavainen (Sun Feb 01 2009 - 01:10:30 CST)
  - Re: [AMBER] Test run on Solaris 10 X 86 Manikandan Chandrasekaran (Mon Feb 02 2009 - 13:16:32 CST)
[AMBER] Question on heating for homology based model. drugdesign (Sat Jan 31 2009 - 12:43:06 CST)
- Re: [AMBER] Question on heating for homology based model. Carlos Simmerling (Sun Feb 01 2009 - 11:47:02 CST)
[AMBER] Can bonded pair of atoms be restrainted by NMR distance restraint? liu junjun (Sun Feb 01 2009 - 01:51:39 CST)
- Re: [AMBER] Can bonded pair of atoms be restrainted by NMR distance restraint? Carlos Simmerling (Sun Feb 01 2009 - 11:55:54 CST)
- Re: [AMBER] Can bonded pair of atoms be restrainted by NMR distance restraint? David A. Case (Sun Feb 01 2009 - 12:35:03 CST)
  - Re: [AMBER] Can bonded pair of atoms be restrainted by NMR distance restraint? liu junjun (Mon Feb 02 2009 - 10:25:41 CST)
[AMBER] the output files oguz gurbulak (Sun Feb 01 2009 - 05:13:02 CST)
- Re: [AMBER] the output files Carlos Simmerling (Sun Feb 01 2009 - 12:11:51 CST)
  - Re: [AMBER] the output files oguz gurbulak (Mon Feb 09 2009 - 07:03:47 CST)
[AMBER] strip frames from crd file aneesh cna (Mon Feb 02 2009 - 03:33:16 CST)
- Re: [AMBER] strip frames from crd file Carlos Simmerling (Mon Feb 02 2009 - 06:12:27 CST)
[AMBER] strip frames from crd file aneesh cna (Mon Feb 02 2009 - 03:35:11 CST)
[AMBER] md simulation on parallel PMEMD oguz gurbulak (Mon Feb 02 2009 - 07:32:31 CST)
- Re: [AMBER] md simulation on parallel PMEMD David A. Case (Mon Feb 02 2009 - 07:54:58 CST)
- Re: [AMBER] md simulation on parallel PMEMD Carlos Simmerling (Mon Feb 02 2009 - 07:55:44 CST)
- Re: [AMBER] md simulation on parallel PMEMD Robert Duke (Mon Feb 02 2009 - 08:03:59 CST)
[AMBER] precision in the trajectory files Jenny Iskrenova (Mon Feb 02 2009 - 08:43:38 CST)
- Re: [AMBER] precision in the trajectory files Adrian Roitberg (Mon Feb 02 2009 - 08:46:49 CST)
- Re: [AMBER] precision in the trajectory files David A. Case (Mon Feb 02 2009 - 08:55:40 CST)
  - Re: [AMBER] precision in the trajectory files Jenny Iskrenova (Tue Feb 03 2009 - 11:07:58 CST)
[AMBER] Radius of Gyration Beale, John (Mon Feb 02 2009 - 11:34:35 CST)
- Re: [AMBER] Radius of Gyration priya priya (Tue Feb 03 2009 - 23:30:07 CST)
[AMBER] Langevin dynamics Antonios Samiotakis (Mon Feb 02 2009 - 11:54:31 CST)
- Re: [AMBER] Langevin dynamics David A. Case (Mon Feb 02 2009 - 13:24:59 CST)
[AMBER] DFT SK parameter for P atom Qizhi Cui (Mon Feb 02 2009 - 13:59:19 CST)
- Re: [AMBER] DFT SK parameter for P atom Adrian Roitberg (Mon Feb 02 2009 - 14:24:00 CST)
  - Re: [AMBER] DFT SK parameter for P atom Qizhi Cui (Mon Feb 02 2009 - 15:37:41 CST)
[AMBER] Micelles set-up?? Alexander Schierholt (Tue Feb 03 2009 - 04:09:52 CST)
[AMBER] creating a restart file from md.out oguz gurbulak (Tue Feb 03 2009 - 04:44:10 CST)
- Re: [AMBER] creating a restart file from md.out Carlos Simmerling (Tue Feb 03 2009 - 05:30:44 CST)
  - Re: [AMBER] creating a restart file from md.out oguz gurbulak (Tue Feb 03 2009 - 07:22:45 CST)
[AMBER] nab compile error with -scalapack chaitanya koppisetty (Tue Feb 03 2009 - 07:23:46 CST)
- Re: [AMBER] nab compile error with -scalapack David A. Case (Tue Feb 03 2009 - 08:27:24 CST)
  - Re: [AMBER] nab compile error with -scalapack chaitanya koppisetty (Tue Feb 03 2009 - 12:52:54 CST)
[AMBER] -MMTSB instalation flag ? Marek Malý (Tue Feb 03 2009 - 09:31:38 CST)
- Re: [AMBER] -MMTSB instalation flag ? Scott Brozell (Tue Feb 03 2009 - 11:06:47 CST)
  - Re: [AMBER] -MMTSB instalation flag ? Marek Malý (Tue Feb 03 2009 - 11:15:04 CST)
    - Re: [AMBER] -MMTSB instalation flag ? Scott Brozell (Tue Feb 03 2009 - 11:38:11 CST)
[AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun drugdesign (Tue Feb 03 2009 - 11:03:20 CST)
- Re: [AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun Ye MEI (Tue Feb 03 2009 - 11:12:54 CST)
  - RE: [AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun Ross Walker (Tue Feb 03 2009 - 11:21:07 CST)
    - Re: [AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun Carlos Simmerling (Tue Feb 03 2009 - 11:39:58 CST)
- Re: [AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun Carlos Simmerling (Tue Feb 03 2009 - 11:17:53 CST)
- Re: [AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun drugdesign (Tue Feb 03 2009 - 23:46:19 CST)
  - Re: [AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun Carlos Simmerling (Wed Feb 04 2009 - 05:16:34 CST)
[AMBER] out error . .. (Tue Feb 03 2009 - 12:58:46 CST)
- Re: [AMBER] out error Carlos Simmerling (Tue Feb 03 2009 - 13:18:39 CST)
[AMBER] MKL error ? Marek Malý (Tue Feb 03 2009 - 17:00:03 CST)
- RE: [AMBER] MKL error ? Ross Walker (Tue Feb 03 2009 - 23:22:48 CST)
  - Re: [AMBER] MKL error ? Marek Malý (Thu Feb 05 2009 - 06:26:05 CST)
    - RE: [AMBER] MKL error ? Ross Walker (Thu Feb 05 2009 - 12:29:45 CST)
    - Re: [AMBER] MKL error ? Marek Malý (Thu Feb 05 2009 - 14:00:10 CST)
[AMBER] a question about umbrella sampling (US) xiaoqin huang (Wed Feb 04 2009 - 11:12:02 CST)
- Re: [AMBER] a question about umbrella sampling (US) Carlos Simmerling (Wed Feb 04 2009 - 11:20:46 CST)
  - RE: [AMBER] a question about umbrella sampling (US) xiaoqin huang (Wed Feb 04 2009 - 16:23:12 CST)
[AMBER] PDB of a specific frame Jason A. Ford-Green (Wed Feb 04 2009 - 13:46:52 CST)
- Re: [AMBER] PDB of a specific frame Carlos Simmerling (Wed Feb 04 2009 - 13:52:49 CST)
[AMBER] compiling errors Gard Nelson (Wed Feb 04 2009 - 18:30:22 CST)
- Re: [AMBER] compiling errors Carlos Simmerling (Wed Feb 04 2009 - 18:35:28 CST)
- RE: [AMBER] compiling errors Ross Walker (Wed Feb 04 2009 - 18:48:14 CST)
[AMBER] Restarting an MD Simulation Hopkins, Robert (Wed Feb 04 2009 - 18:34:16 CST)
- RE: [AMBER] Restarting an MD Simulation Ross Walker (Wed Feb 04 2009 - 21:03:36 CST)
  - RE: [AMBER] Restarting an MD Simulation Ross Walker (Wed Feb 04 2009 - 21:24:56 CST)
[AMBER] pmemd installation in intelmpi Vijay Manickam Achari (Wed Feb 04 2009 - 21:16:06 CST)
- Re: [AMBER] pmemd installation in intelmpi Robert Duke (Wed Feb 04 2009 - 22:34:37 CST)
  - Re: [AMBER] pmemd installation in intelmpi Vijay Manickam Achari (Thu Feb 05 2009 - 02:38:38 CST)
[AMBER] Compiling Carnal Amber7 in Amber9 Vijay Manickam Achari (Wed Feb 04 2009 - 21:21:14 CST)
- RE: [AMBER] Compiling Carnal Amber7 in Amber9 Bill Ross (Wed Feb 11 2009 - 13:04:53 CST)
  - RE: [AMBER] Compiling Carnal Amber7 in Amber9 Vijay Manickam Achari (Thu Feb 12 2009 - 03:12:29 CST)
    - Re: [AMBER] Compiling Carnal Amber7 in Amber9 David A. Case (Thu Feb 12 2009 - 06:58:03 CST)
    - RE: [AMBER] Compiling Carnal Amber7 in Amber9 Ross Walker (Thu Feb 12 2009 - 08:55:54 CST)
- RE: [AMBER] Compiling Carnal Amber7 in Amber9 Bill Ross (Thu Feb 12 2009 - 14:32:29 CST)
[AMBER] production run terminates due to (*) symbols in xxx.rst Vijay Manickam Achari (Wed Feb 04 2009 - 22:17:38 CST)
- Re: [AMBER] production run terminates due to (*) symbols in xxx.rst vallespardojl_at_chem.leidenuniv.nl (Thu Feb 05 2009 - 04:28:33 CST)
  - Re: [AMBER] production run terminates due to (*) symbols in xxx.rst Vijay Manickam Achari (Thu Feb 05 2009 - 04:58:26 CST)
- Re: [AMBER] production run terminates due to (*) symbols in xxx.rst Bill Ross (Thu Feb 05 2009 - 11:42:55 CST)
  - Re: [AMBER] production run terminates due to (*) symbols in xxx.rst Vijay Manickam Achari (Thu Feb 05 2009 - 20:50:20 CST)
- RE: [AMBER] production run terminates due to (*) symbols in xxx.rst Ross Walker (Thu Feb 05 2009 - 12:58:41 CST)
[AMBER] how can i deal with large number atoms Wang,Ying (Wed Feb 04 2009 - 23:04:23 CST)
[AMBER] How to build reference coordinate file for targeted MD gmail (Thu Feb 05 2009 - 00:44:22 CST)
- Re: [AMBER] How to build reference coordinate file for targeted MD Carlos Simmerling (Thu Feb 05 2009 - 05:19:12 CST)
  - Re: [AMBER] How to build reference coordinate file for targeted MD xiaonan zhang (Thu Feb 05 2009 - 06:00:38 CST)
  - Re: [AMBER] How to build reference coordinate file for targeted MD gmail (Thu Feb 05 2009 - 23:20:59 CST)
    - RE: [AMBER] How to build reference coordinate file for targeted MD Ross Walker (Fri Feb 06 2009 - 02:14:14 CST)
[AMBER] error in executing sander.MPI in amber9 Vijay Manickam Achari (Thu Feb 05 2009 - 02:37:09 CST)
- Re: [AMBER] error in executing sander.MPI in amber9 Atro Tossavainen (Thu Feb 05 2009 - 05:08:59 CST)
[AMBER] Solvation potential and free energies guardiani_at_fi.infn.it (Thu Feb 05 2009 - 06:27:21 CST)
- Re: [AMBER] Solvation potential and free energies Carlos Simmerling (Thu Feb 05 2009 - 06:33:08 CST)
- Re: [AMBER] Solvation potential and free energies Lorenzo Gontrani (Thu Feb 05 2009 - 06:34:47 CST)
- Re: [AMBER] Solvation potential and free energies David A. Case (Fri Feb 06 2009 - 07:34:25 CST)
[AMBER] parameter files for D-amino acid Vsatheesh Patil (Thu Feb 05 2009 - 07:04:12 CST)
- Re: [AMBER] parameter files for D-amino acid Carlos Simmerling (Thu Feb 05 2009 - 07:37:32 CST)
  - Re: [AMBER] parameter files for D-amino acid vijayaraj_at_clri.res.in (Thu Feb 05 2009 - 08:49:56 CST)
[AMBER] pmemd on BlueGene/P? Hannes Loeffler (Thu Feb 05 2009 - 07:09:45 CST)
- Re: [AMBER] pmemd on BlueGene/P? Robert Duke (Thu Feb 05 2009 - 07:42:32 CST)
- Re: [AMBER] pmemd on BlueGene/P? Carlos P Sosa (Thu Feb 05 2009 - 14:48:57 CST)
  - Re: [AMBER] pmemd on BlueGene/P? Hannes Loeffler (Fri Feb 06 2009 - 03:01:37 CST)
Re: [AMBER] Compiling Carnal Amber7 in Amber9 Bill Ross (Thu Feb 05 2009 - 11:36:00 CST)
- Re: [AMBER] Compiling Carnal Amber7 in Amber9 Vijay Manickam Achari (Wed Feb 11 2009 - 01:58:08 CST)
  - RE: [AMBER] Compiling Carnal Amber7 in Amber9 Ross Walker (Wed Feb 11 2009 - 10:53:10 CST)
[AMBER] amber9 installation problem in SMP IA64 Vijay Manickam Achari (Fri Feb 06 2009 - 01:00:16 CST)
- Re: [AMBER] amber9 installation problem in SMP IA64 David A. Case (Fri Feb 06 2009 - 07:25:55 CST)
  - Re: [AMBER] amber9 installation problem in SMP IA64 Vijay Manickam Achari (Tue Feb 10 2009 - 02:30:55 CST)
[AMBER] mpirun problem in HPC Vijay Manickam Achari (Fri Feb 06 2009 - 01:01:29 CST)
- RE: [AMBER] mpirun problem in HPC Ross Walker (Fri Feb 06 2009 - 02:05:37 CST)
[AMBER] second derivative matrix calculation Marie Brut (Fri Feb 06 2009 - 04:47:18 CST)
- Re: [AMBER] second derivative matrix calculation David A. Case (Fri Feb 06 2009 - 07:19:52 CST)
[AMBER] extract frames from a .mdcrd vallespardojl_at_chem.leidenuniv.nl (Fri Feb 06 2009 - 04:48:23 CST)
- Re: [AMBER] extract frames from a .mdcrd Carlos Simmerling (Fri Feb 06 2009 - 05:12:00 CST)
  - Re: [AMBER] extract frames from a .mdcrd vallespardojl_at_chem.leidenuniv.nl (Tue Feb 10 2009 - 02:52:19 CST)
    - Re: [AMBER] extract frames from a .mdcrd Carlos Simmerling (Tue Feb 10 2009 - 04:58:12 CST)
- Re: [AMBER] extract frames from a .mdcrd Bill Ross (Fri Feb 06 2009 - 13:13:27 CST)
[AMBER] MSD and stress tensors oguz gurbulak (Fri Feb 06 2009 - 05:09:12 CST)
[AMBER] script to convert GLYCAM ff in CHARMM format ABEL Stephane 175950 (Fri Feb 06 2009 - 08:39:04 CST)
- Re: [AMBER] script to convert GLYCAM ff in CHARMM format Lachele Foley (Lists) (Fri Feb 06 2009 - 08:57:17 CST)
  - RE : [AMBER] script to convert GLYCAM ff in CHARMM format ABEL Stephane 175950 (Fri Feb 06 2009 - 09:03:19 CST)
[AMBER] Resp charge . .. (Fri Feb 06 2009 - 11:34:12 CST)
- Re: [AMBER] Resp charge Jason A. Ford-Green (Fri Feb 06 2009 - 14:38:29 CST)
[AMBER] ptraj fails to recognize binary REMD output Kevin Wiehe (Fri Feb 06 2009 - 11:44:21 CST)
[AMBER] distance calculation by reading in the restraint file xiaoqin huang (Fri Feb 06 2009 - 11:52:56 CST)
- RE: [AMBER] distance calculation by reading in the restraint file xiaoqin huang (Fri Feb 06 2009 - 12:34:34 CST)
  - Re: [AMBER] distance calculation by reading in the restraint file David A. Case (Fri Feb 06 2009 - 16:35:55 CST)
    - RE: [AMBER] distance calculation by reading in the restraint file xiaoqin huang (Fri Feb 06 2009 - 17:28:59 CST)
- Re: [AMBER] distance calculation by reading in the restraint file David A. Case (Fri Feb 06 2009 - 16:03:08 CST)
[AMBER] MD analysis oguz gurbulak (Sat Feb 07 2009 - 08:56:10 CST)
[AMBER] Stability of a long NPT md trajectory? Bill K (Mon Feb 09 2009 - 01:07:24 CST)
- Re: [AMBER] Stability of a long NPT md trajectory? Carlos Simmerling (Mon Feb 09 2009 - 06:08:29 CST)
  - Re: [AMBER] Stability of a long NPT md trajectory? Robert Duke (Mon Feb 09 2009 - 07:25:10 CST)
[AMBER] second derivative matrix Marie Brut (Mon Feb 09 2009 - 02:53:01 CST)
- Re: [AMBER] second derivative matrix Adrian Roitberg (Mon Feb 09 2009 - 08:29:51 CST)
- Re: [AMBER] second derivative matrix David A. Case (Mon Feb 09 2009 - 09:05:18 CST)
[AMBER] NAB md function prints strange output Jochen Heil (Mon Feb 09 2009 - 05:30:21 CST)
- Re: [AMBER] NAB md function prints strange output David A. Case (Mon Feb 09 2009 - 06:58:43 CST)
  - Re: [AMBER] NAB md function prints strange output Jochen Heil (Tue Feb 10 2009 - 06:19:56 CST)
    - Re: [AMBER] NAB md function prints strange output David A. Case (Tue Feb 10 2009 - 06:46:40 CST)
    - Re: [AMBER] NAB md function prints strange output Scott Brozell (Thu Mar 12 2009 - 16:04:15 CDT)
[AMBER] APS & ff03 Mahmoud A. A. Ibrahim (Mon Feb 09 2009 - 08:49:56 CST)
[AMBER] parmchk s. Bill (Mon Feb 09 2009 - 09:55:20 CST)
- RE: [AMBER] parmchk Ross Walker (Mon Feb 09 2009 - 10:28:20 CST)
[AMBER] hbond analysis aneesh cna (Mon Feb 09 2009 - 11:55:25 CST)
- Re: [AMBER] hbond analysis Bala subramanian (Mon Feb 09 2009 - 12:33:39 CST)
- Re: [AMBER] hbond analysis Carlos Simmerling (Mon Feb 09 2009 - 12:52:14 CST)
[AMBER] Solvating inside of a channel Daniel Smith (Mon Feb 09 2009 - 15:03:16 CST)
[AMBER] Confusion regarding box size parul sharma (Tue Feb 10 2009 - 01:20:01 CST)
- Re: [AMBER] Confusion regarding box size vallespardojl_at_chem.leidenuniv.nl (Tue Feb 10 2009 - 02:35:24 CST)
- Re: [AMBER] Confusion regarding box size Wei Zhang (Tue Feb 10 2009 - 07:07:38 CST)
  - Re: [AMBER] Confusion regarding box size parul sharma (Tue Feb 10 2009 - 07:29:38 CST)
[AMBER] Irregularity in box during md parul sharma (Tue Feb 10 2009 - 04:35:18 CST)
- Re: [AMBER] Irregularity in box during md Carlos Simmerling (Tue Feb 10 2009 - 04:57:02 CST)
- Re: [AMBER] Irregularity in box during md Bill Ross (Tue Feb 10 2009 - 11:24:12 CST)
[AMBER] RED-vIII: Scratch directory for Gaussian [NOT FOUND] Patrick Schopf (Tue Feb 10 2009 - 08:15:42 CST)
- RE : [AMBER] RED-vIII: Scratch directory for Gaussian [NOT FOUND] ABEL Stephane 175950 (Tue Feb 10 2009 - 08:39:17 CST)
- Re: [AMBER] RED-vIII: Scratch directory for Gaussian [NOT FOUND] FyD (Tue Feb 10 2009 - 09:05:56 CST)
[AMBER] Scaling of dipole interactions Diddo Diddens (Tue Feb 10 2009 - 08:33:18 CST)
[AMBER] formate parameters Dmitri Nilov (Tue Feb 10 2009 - 08:47:31 CST)
[AMBER] array out of bound in Amber10 tests Shan-ho Tsai (Tue Feb 10 2009 - 10:19:42 CST)
- Re: [AMBER] array out of bound in Amber10 tests David A. Case (Tue Feb 10 2009 - 10:39:43 CST)
  - Re: [AMBER] array out of bound in Amber10 tests Shan-ho Tsai (Tue Feb 10 2009 - 15:04:43 CST)
[AMBER] reg . run TMD balaji nagarajan (Tue Feb 10 2009 - 11:36:28 CST)
- Re: [AMBER] reg . run TMD Carlos Simmerling (Tue Feb 10 2009 - 11:48:22 CST)
[AMBER] Solvating the interior of a channel Daniel Smith (Tue Feb 10 2009 - 14:42:09 CST)
- Re: [AMBER] Solvating the interior of a channel Shozeb Haider (Wed Feb 11 2009 - 07:15:07 CST)
- Re: [AMBER] Solvating the interior of a channel Jason A. Ford-Green (Wed Feb 11 2009 - 10:04:24 CST)
  - Re: [AMBER] Solvating the interior of a channel Daniel Smith (Fri Feb 13 2009 - 15:02:24 CST)
    - Re: [AMBER] Solvating the interior of a channel Daniel Smith (Sun Feb 15 2009 - 16:40:23 CST)
[AMBER] AMBER: chiral restraint on protein amit jain (Tue Feb 10 2009 - 18:48:12 CST)
- Re: [AMBER] AMBER: chiral restraint on protein David A. Case (Wed Feb 11 2009 - 06:56:05 CST)
[AMBER] how to get amber 10 Prem Prakash Pathak (Tue Feb 10 2009 - 20:42:37 CST)
- RE: [AMBER] how to get amber 10 Ross Walker (Tue Feb 10 2009 - 21:20:33 CST)
[AMBER] nmr refinement of dimer Sally Pias (Wed Feb 11 2009 - 03:05:56 CST)
- Re: [AMBER] nmr refinement of dimer Therese Malliavin (Wed Feb 11 2009 - 04:57:06 CST)
- Re: [AMBER] nmr refinement of dimer David A. Case (Wed Feb 11 2009 - 07:02:37 CST)
  - Re: [AMBER] nmr refinement of dimer Sally Pias (Thu Feb 12 2009 - 03:17:44 CST)
    - Re: [AMBER] nmr refinement of dimer David A. Case (Thu Feb 12 2009 - 07:08:08 CST)
[AMBER] lmod calculation for complexe . .. (Wed Feb 11 2009 - 03:09:04 CST)
[AMBER] Optimization problem Daniel Emery (Thu Feb 12 2009 - 04:01:49 CST)
- Re: [AMBER] Optimization problem David A. Case (Thu Feb 12 2009 - 06:58:17 CST)
  - Re: [AMBER] Optimization problem Daniel Emery (Thu Feb 12 2009 - 08:11:14 CST)
- Re: [AMBER] Optimization problem Gustavo Seabra (Thu Feb 12 2009 - 08:48:23 CST)
[AMBER] error in xleap: ligand binding using MMand QMMM tech kureeckal ramesh (Thu Feb 12 2009 - 04:27:41 CST)
- Re: [AMBER] error in xleap: ligand binding using MMand QMMM tech Gustavo Seabra (Thu Feb 12 2009 - 08:32:17 CST)
[AMBER] H-bond information Beale, John (Thu Feb 12 2009 - 09:32:30 CST)
[AMBER] projections of trajectories onto the first 2 principal eigenvectors Carra, Claudio (JSC-SK)[USRA] (Thu Feb 12 2009 - 12:22:20 CST)
- Re: [AMBER] projections of trajectories onto the first 2 principal eigenvectors Hannes Loeffler (Fri Feb 13 2009 - 02:32:20 CST)
  - Re: [AMBER] projections of trajectories onto the first 2 principal eigenvectors Hannes Loeffler (Fri Feb 13 2009 - 03:33:19 CST)
[AMBER] atoms fly out of the box in NVT calculations iccy liu (Thu Feb 12 2009 - 15:48:24 CST)
- Re: [AMBER] atoms fly out of the box in NVT calculations Carlos Simmerling (Thu Feb 12 2009 - 16:05:10 CST)
- Re: [AMBER] atoms fly out of the box in NVT calculations Ross Walker (Thu Feb 12 2009 - 20:22:57 CST)
  - RE: [AMBER] atoms fly out of the box in NVT calculations iccy liu (Sun Feb 15 2009 - 17:34:37 CST)
[AMBER] How to jude whether the trajectory is stable or not Jeffrey (Thu Feb 12 2009 - 20:33:53 CST)
[AMBER] Beginner question Heath Watts (Fri Feb 13 2009 - 15:18:42 CST)
- Re: [AMBER] Beginner question Carlos Simmerling (Fri Feb 13 2009 - 15:24:37 CST)
  - Re: [AMBER] Beginner question Heath Watts (Fri Feb 13 2009 - 19:19:44 CST)
- Re: [AMBER] Beginner question Barbault Florent (Fri Feb 13 2009 - 15:25:13 CST)
  - Re: [AMBER] Beginner question Heath Watts (Fri Feb 13 2009 - 19:20:46 CST)
[AMBER] Question about improper torsions... Antonios Samiotakis (Fri Feb 13 2009 - 16:57:03 CST)
- Re: [AMBER] Question about improper torsions... David A. Case (Sat Feb 14 2009 - 07:32:21 CST)
[AMBER] New atom type with 7 bonds Akansha Saxena (Fri Feb 13 2009 - 17:56:47 CST)
- Re: [AMBER] New atom type with 7 bonds David A. Case (Mon Feb 16 2009 - 08:28:25 CST)
[AMBER] install Amber 10 to Macbook Adrien Delmont (Sat Feb 14 2009 - 05:06:50 CST)
- Re: [AMBER] install Amber 10 to Macbook David A. Case (Sat Feb 14 2009 - 17:17:53 CST)
  - Re: [AMBER] install Amber 10 to Macbook Tyler Luchko (Sun Feb 15 2009 - 13:27:53 CST)
    - Re: [AMBER] install Amber 10 to Macbook David Watson (Sun Feb 15 2009 - 13:52:36 CST)
[AMBER] Any link to a major QM code? Francesco Pietra (Sun Feb 15 2009 - 11:58:30 CST)
- Re: [AMBER] Any link to a major QM code? Gustavo Seabra (Sun Feb 15 2009 - 18:17:32 CST)
  - Re: [AMBER] Any link to a major QM code? Adrian Roitberg (Sun Feb 15 2009 - 20:59:01 CST)
    - Re: [AMBER] Any link to a major QM code? Francesco Pietra (Mon Feb 16 2009 - 08:47:04 CST)
    - Re: [AMBER] Any link to a major QM code? Gustavo Seabra (Mon Feb 16 2009 - 10:51:03 CST)
[AMBER] Error running sander.MPI Vijay Manickam Achari (Mon Feb 16 2009 - 02:23:05 CST)
- Re: [AMBER] Error running sander.MPI Carlos Simmerling (Mon Feb 16 2009 - 05:51:08 CST)
- RE: [AMBER] Error running sander.MPI Rausch, Felix (Tue Feb 17 2009 - 02:15:19 CST)
  - Re: [AMBER] Error running sander.MPI Anselm Horn (Tue Feb 17 2009 - 04:28:47 CST)
[AMBER] Error installing Amber David Patiño (Mon Feb 16 2009 - 06:02:31 CST)
- Re: [AMBER] Error installing Amber David A. Case (Mon Feb 16 2009 - 08:21:41 CST)
  - Re: [AMBER] Error installing Amber David Patiño (Tue Feb 17 2009 - 08:58:05 CST)
[AMBER] Iron 2+ parameters Hrvoje Brkiæ (Mon Feb 16 2009 - 07:53:57 CST)
- Re: [AMBER] Iron 2+ parameters Syed Tarique Moin (Mon Feb 16 2009 - 10:25:34 CST)
- Re: [AMBER] Iron 2+ parameters FyD (Mon Feb 16 2009 - 12:25:45 CST)
[AMBER] density and volume in NVT ensamble oguz gurbulak (Mon Feb 16 2009 - 07:58:13 CST)
- Re: [AMBER] density and volume in NVT ensamble Carlos Simmerling (Mon Feb 16 2009 - 08:04:22 CST)
  - Re: [AMBER] density and volume in NVT ensamble oguz gurbulak (Mon Feb 16 2009 - 08:25:52 CST)
- Re: [AMBER] density and volume in NVT ensamble Andrew Purkiss-Trew (Mon Feb 16 2009 - 08:14:40 CST)
  - Re: [AMBER] density and volume in NVT ensamble oguz gurbulak (Mon Feb 16 2009 - 08:32:07 CST)
    - Re: [AMBER] density and volume in NVT ensamble Andrew Purkiss-Trew (Mon Feb 16 2009 - 08:45:25 CST)
[AMBER] contant force pulling simulation with amber 10 li hui (Mon Feb 16 2009 - 11:01:36 CST)
- Re: [AMBER] contant force pulling simulation with amber 10 Gustavo Seabra (Mon Feb 16 2009 - 12:11:40 CST)
[AMBER] can ptraj output the trajectory of the residue CM? Jose Borreguero (Mon Feb 16 2009 - 13:47:34 CST)
[AMBER] using ptraj Molecular Dynamics (Mon Feb 16 2009 - 14:31:42 CST)
- Re: [AMBER] using ptraj Carlos Simmerling (Mon Feb 16 2009 - 14:41:54 CST)
  - Re: [AMBER] using ptraj Molecular Dynamics (Tue Feb 17 2009 - 05:44:09 CST)
[AMBER] Normal errors on job kill? ben rodriguez (Mon Feb 16 2009 - 20:35:43 CST)
- Re: [AMBER] Normal errors on job kill? David A. Case (Mon Feb 16 2009 - 22:25:54 CST)
[AMBER] Amber 9 Install - AMBERBUILDFLAGS error ben rodriguez (Mon Feb 16 2009 - 21:39:14 CST)
- Re: [AMBER] Amber 9 Install - AMBERBUILDFLAGS error David A. Case (Mon Feb 16 2009 - 22:29:41 CST)
[AMBER] parallel run error balaji nagarajan (Tue Feb 17 2009 - 02:19:23 CST)
- Re: [AMBER] parallel run error Carlos Simmerling (Tue Feb 17 2009 - 06:40:03 CST)
[AMBER] constph tutorial help Prem Prakash Pathak (Tue Feb 17 2009 - 06:53:37 CST)
[AMBER] (no subject) Beale, John (Tue Feb 17 2009 - 07:02:25 CST)
- Re: [AMBER] (no subject) Carlos Simmerling (Tue Feb 17 2009 - 07:10:49 CST)
[AMBER] MD simulation with a partially flexible system Jeffrey (Tue Feb 17 2009 - 08:38:10 CST)
- Re: [AMBER] MD simulation with a partially flexible system Carlos Simmerling (Tue Feb 17 2009 - 08:45:33 CST)
  - Re: Re: [AMBER] MD simulation with a partially flexible system Jeffrey (Tue Feb 17 2009 - 20:19:47 CST)
    - Re: Re: [AMBER] MD simulation with a partially flexible system Carlos Simmerling (Wed Feb 18 2009 - 06:35:40 CST)
[AMBER] DM complexation . .. (Tue Feb 17 2009 - 09:10:49 CST)
- Re: [AMBER] DM complexation Carlos Simmerling (Tue Feb 17 2009 - 09:28:34 CST)
  - RE: [AMBER] DM complexation . .. (Tue Feb 17 2009 - 09:36:01 CST)
    - Re: [AMBER] DM complexation Carlos Simmerling (Tue Feb 17 2009 - 09:59:15 CST)
[AMBER] How to get the energy of a molecule in a whole system Wang,Ying (Tue Feb 17 2009 - 10:28:39 CST)
[AMBER] restraint angle m m (Tue Feb 17 2009 - 11:17:00 CST)
- Re: [AMBER] restraint angle David A. Case (Tue Feb 17 2009 - 11:52:49 CST)
[AMBER] PMF calculation Arnaud (Tue Feb 17 2009 - 12:10:18 CST)
- Re: [AMBER] PMF calculation David A. Case (Tue Feb 17 2009 - 20:23:20 CST)
[AMBER] Need suggestion on payment for Ph.D student majored in molecular simulation Xu Dong (Tue Feb 17 2009 - 12:54:58 CST)
- Re: [AMBER] Need suggestion on payment for Ph.D student majored in molecular simulation Adrian Roitberg (Tue Feb 17 2009 - 12:57:56 CST)
[AMBER] glycam and solvateoct command Heath Watts (Tue Feb 17 2009 - 13:51:13 CST)
- Re: [AMBER] glycam and solvateoct command Barbault Florent (Tue Feb 17 2009 - 14:13:58 CST)
  - Re: [AMBER] glycam and solvateoct command Heath Watts (Tue Feb 17 2009 - 16:31:35 CST)
    - Re: [AMBER] glycam and solvateoct command Lachele Foley (Lists) (Wed Feb 18 2009 - 09:00:34 CST)
[AMBER] problem compiling nmode.c Shan-ho Tsai (Tue Feb 17 2009 - 14:38:00 CST)
- Re: [AMBER] problem compiling nmode.c David A. Case (Tue Feb 17 2009 - 20:45:03 CST)
  - [AMBER] NVT vs NPT Chih-Ying Lin (Tue Feb 17 2009 - 21:23:05 CST)
  - Re: [AMBER] problem compiling nmode.c Shan-ho Tsai (Thu Feb 19 2009 - 08:49:39 CST)
[AMBER] reg.Targeted molecular dynamics balaji nagarajan (Tue Feb 17 2009 - 23:26:49 CST)
- Re: [AMBER] reg.Targeted molecular dynamics Simon Becker (Wed Feb 18 2009 - 05:38:54 CST)
  - RE: [AMBER] reg.Targeted molecular dynamics balaji nagarajan (Wed Feb 18 2009 - 08:07:09 CST)
[AMBER] protein monomerizartion times and simulation with implicit solvent drugdesign (Wed Feb 18 2009 - 04:27:17 CST)
- Re: [AMBER] protein monomerizartion times and simulation with implicit solvent Carlos Simmerling (Wed Feb 18 2009 - 06:16:00 CST)
[AMBER] Re: AMBER: GBSA EGB = NaN Markus Kaukonen (Wed Feb 18 2009 - 06:26:28 CST)
- [AMBER] Re: AMBER: GBSA EGB = NaN Markus Kaukonen (Thu Feb 19 2009 - 07:34:38 CST)
[AMBER] IG not change at each restart of NPT simulation Jeffrey (Wed Feb 18 2009 - 06:49:47 CST)
- Re: [AMBER] IG not change at each restart of NPT simulation Robert Duke (Wed Feb 18 2009 - 07:57:35 CST)
  - Re: [AMBER] IG not change at each restart of NPT simulation Carlos Simmerling (Wed Feb 18 2009 - 08:04:47 CST)
    - Re: [AMBER] IG not change at each restart of NPT simulation Robert Duke (Wed Feb 18 2009 - 08:15:00 CST)
    - Re: [AMBER] IG not change at each restart of NPT simulation Adrian Roitberg (Wed Feb 18 2009 - 08:46:36 CST)
- Re: [AMBER] IG not change at each restart of NPT simulation Hopkins, Robert (Wed Mar 18 2009 - 17:55:33 CDT)
  - RE: [AMBER] IG not change at each restart of NPT simulation Ross Walker (Wed Mar 18 2009 - 18:07:07 CDT)
[AMBER] How to constrain the hydrogen bonding distances... Majeed Shaik (Wed Feb 18 2009 - 08:11:37 CST)
- Re: [AMBER] How to constrain the hydrogen bonding distances... Carlos Simmerling (Wed Feb 18 2009 - 08:25:47 CST)
- Re: [AMBER] How to constrain the hydrogen bonding distances... David A. Case (Wed Feb 18 2009 - 08:28:56 CST)
[AMBER] ./configure_amber: line 1211: cd: netcdf/src: No such file or directory Andrew Olson (Wed Feb 18 2009 - 11:08:57 CST)
- Re: [AMBER] ./configure_amber: line 1211: cd: netcdf/src: No such file or directory David A. Case (Wed Feb 18 2009 - 12:11:56 CST)
[AMBER] question about ptraj hydrogen bond analysis monica bhattacharee (Wed Feb 18 2009 - 13:45:17 CST)
- Re: [AMBER] question about ptraj hydrogen bond analysis Thomas Cheatham III (Wed Feb 18 2009 - 14:21:27 CST)
[AMBER] (NTB /= 0 && NTP /= 0) but IFBOX == 0 error Majeed Shaik (Wed Feb 18 2009 - 14:09:17 CST)
- Re: [AMBER] (NTB /= 0 && NTP /= 0) but IFBOX == 0 error David A. Case (Wed Feb 18 2009 - 14:35:12 CST)
[AMBER] Re: AMBER: How do you evaluate forces on a fixed atom? Bill Kowallis (Wed Feb 18 2009 - 19:55:47 CST)
[AMBER] test charge Dan Kaps (Wed Feb 18 2009 - 20:27:32 CST)
- Re: [AMBER] test charge David A. Case (Wed Feb 18 2009 - 22:24:04 CST)
  - Re: [AMBER] test charge Dan Kaps (Thu Feb 19 2009 - 20:22:31 CST)
[AMBER] distance matrix plot and secondary structure analysis Siddharth Rastogi (Thu Feb 19 2009 - 00:17:47 CST)
- Re: [AMBER] distance matrix plot and secondary structure analysis Carlos Simmerling (Thu Feb 19 2009 - 06:48:57 CST)
[AMBER] Protein motions comparison Dmitry Osolodkin (Thu Feb 19 2009 - 05:58:24 CST)
- Re: [AMBER] Protein motions comparison Hannes Loeffler (Thu Feb 19 2009 - 06:07:47 CST)
[AMBER] secstruct Beale, John (Thu Feb 19 2009 - 07:22:20 CST)
- Re: [AMBER] secstruct Carlos Simmerling (Thu Feb 19 2009 - 07:30:16 CST)
[AMBER] dipole correlation function Jeffrey (Thu Feb 19 2009 - 08:18:20 CST)
- Re: [AMBER] dipole correlation function Carlos Simmerling (Thu Feb 19 2009 - 08:39:16 CST)
  - Re: Re: [AMBER] dipole correlation function Jeffrey (Thu Feb 19 2009 - 10:39:15 CST)
[AMBER] paper of interest for FF development/solvent models David Mobley (Thu Feb 19 2009 - 09:15:04 CST)
[AMBER] (no subject) Andrew Olson (Thu Feb 19 2009 - 13:46:24 CST)
[AMBER] Antechamber kureeckal ramesh (Thu Feb 19 2009 - 19:36:03 CST)
[AMBER] Problem with NVT and NPT parul sharma (Fri Feb 20 2009 - 07:07:36 CST)
- Re: [AMBER] Problem with NVT and NPT Adrian Roitberg (Fri Feb 20 2009 - 07:14:23 CST)
  - Re: [AMBER] Problem with NVT and NPT parul sharma (Fri Feb 20 2009 - 07:27:51 CST)
    - Re: [AMBER] Problem with NVT and NPT Carlos Simmerling (Fri Feb 20 2009 - 07:30:26 CST)
[AMBER] Parmchk wrongly calculates missing parameters (fwd) Gijs Schaftenaar (Fri Feb 20 2009 - 07:16:17 CST)
[AMBER] ACS computational chemistry awards - March 9th deadline Carlos Simmerling (Fri Feb 20 2009 - 10:27:18 CST)
[AMBER] order of "upper" and "lower" bounds in the makeDIS_RST inputs Piotr Cieplak (Fri Feb 20 2009 - 15:40:14 CST)
- Re: [AMBER] order of "upper" and "lower" bounds in the makeDIS_RST inputs David A. Case (Sat Feb 21 2009 - 17:51:38 CST)
[AMBER] reg.targeted molecular dynamics balaji nagarajan (Fri Feb 20 2009 - 23:10:50 CST)
- Re: [AMBER] reg.targeted molecular dynamics Carlos Simmerling (Sat Feb 21 2009 - 06:35:05 CST)
  - RE: [AMBER] reg.targeted molecular dynamics balaji nagarajan (Sun Feb 22 2009 - 08:45:29 CST)
[AMBER] A beginner's question for using AMBER to do cell membrane simulation and molecular transportation Xu Dong (Sat Feb 21 2009 - 14:27:29 CST)
- Re: [AMBER] A beginner's question for using AMBER to do cell membrane simulation and molecular transportation Carlos Simmerling (Sat Feb 21 2009 - 15:33:31 CST)
  - Re: [AMBER] A beginner's question for using AMBER to do cell membrane simulation and molecular transportation Xu Dong (Sat Feb 21 2009 - 15:40:03 CST)
[AMBER] PME doesn't work parul sharma (Mon Feb 23 2009 - 03:43:40 CST)
- Re: [AMBER] PME doesn't work Carlos Simmerling (Mon Feb 23 2009 - 05:19:27 CST)
  - Re: [AMBER] PME doesn't work parul sharma (Mon Feb 23 2009 - 06:03:54 CST)
    - Re: [AMBER] PME doesn't work Carlos Simmerling (Mon Feb 23 2009 - 06:08:07 CST)
- Re: [AMBER] PME doesn't work Robert Duke (Mon Feb 23 2009 - 07:48:04 CST)
[AMBER] PMEMD vs GROMACS? Sasha Buzko (Mon Feb 23 2009 - 13:55:27 CST)
- Re: [AMBER] PMEMD vs GROMACS? Vlad Cojocaru (Tue Feb 24 2009 - 02:24:16 CST)
  - Re: [AMBER] PMEMD vs GROMACS? Hannes Loeffler (Tue Feb 24 2009 - 02:39:29 CST)
    - Re: [AMBER] PMEMD vs GROMACS? Vlad Cojocaru (Tue Feb 24 2009 - 02:46:36 CST)
  - Re: [AMBER] PMEMD vs GROMACS? Sasha Buzko (Tue Feb 24 2009 - 11:15:59 CST)
[AMBER] problem with amber installation nicholus bhattacharjee (Tue Feb 24 2009 - 00:50:12 CST)
- Re: [AMBER] problem with amber installation Carlos Simmerling (Tue Feb 24 2009 - 05:47:20 CST)
  - Re: [AMBER] problem with amber installation nicholus bhattacharjee (Tue Feb 24 2009 - 22:29:11 CST)
[AMBER] follow-up to previous discussion: nmr refinement of dimer Sally Pias (Tue Feb 24 2009 - 01:50:41 CST)
- Re: [AMBER] follow-up to previous discussion: nmr refinement of dimer David A. Case (Tue Feb 24 2009 - 07:15:27 CST)
[AMBER] About the croase grainded FF James W (Tue Feb 24 2009 - 01:58:12 CST)
- Re: [AMBER] About the croase grainded FF Vlad Cojocaru (Tue Feb 24 2009 - 02:40:53 CST)
[AMBER] (no subject) Beale, John (Tue Feb 24 2009 - 05:59:51 CST)
[AMBER] amber tools reading netcdf files Jeremy Harris (Tue Feb 24 2009 - 09:54:09 CST)
- Re: [AMBER] amber tools reading netcdf files Chris Moth (Tue Feb 24 2009 - 11:35:22 CST)
  - RE: [AMBER] amber tools reading netcdf files Cojocaru,Vlad (Tue Feb 24 2009 - 12:46:27 CST)
[AMBER] perform an analysis using ptraj oguz gurbulak (Tue Feb 24 2009 - 10:19:11 CST)
[AMBER] Equilibration Scaling to System Size Hopkins, Robert (Tue Feb 24 2009 - 16:31:37 CST)
- Re: [AMBER] Equilibration Scaling to System Size Carlos Simmerling (Tue Feb 24 2009 - 16:49:10 CST)
[AMBER] problem about trajectory analysis Adrien Delmont (Wed Feb 25 2009 - 08:24:41 CST)
- Re: [AMBER] problem about trajectory analysis Thomas Cheatham III (Wed Feb 25 2009 - 18:57:49 CST)
[AMBER] (no subject) waleed zalloum (Wed Feb 25 2009 - 10:41:14 CST)
- Re: [AMBER] (no subject) Thomas Cheatham III (Wed Feb 25 2009 - 18:48:56 CST)
[AMBER] ptraj analyze Beale, John (Wed Feb 25 2009 - 10:56:59 CST)
- Re: [AMBER] ptraj analyze Thomas Cheatham III (Wed Feb 25 2009 - 18:45:17 CST)
[AMBER] Simulated annealing Ibrahim Moustafa (Wed Feb 25 2009 - 18:26:37 CST)
- Re: [AMBER] Simulated annealing Carlos Simmerling (Wed Feb 25 2009 - 19:31:30 CST)
  - Re: [AMBER] Simulated annealing Ibrahim Moustafa (Thu Feb 26 2009 - 09:28:44 CST)
[AMBER] Error in using Amber sri noraima othman (Wed Feb 25 2009 - 21:27:29 CST)
- RE: [AMBER] Error in using Amber Ross Walker (Thu Feb 26 2009 - 00:03:12 CST)
  - Re: [AMBER] Error in using Amber sri noraima othman (Thu Feb 26 2009 - 00:27:14 CST)
[AMBER] tleap errors !! Sampath Koppole (Thu Feb 26 2009 - 03:47:48 CST)
- Re: [AMBER] tleap errors !! David A. Case (Thu Feb 26 2009 - 07:45:49 CST)
[AMBER] MD simulation at constant pH Francesco Pietra (Thu Feb 26 2009 - 04:52:47 CST)
[AMBER] Current Amber10 bugfix.all doesn't apply cleanly Mark Dixon (Thu Feb 26 2009 - 05:54:03 CST)
- Re: [AMBER] Current Amber10 bugfix.all doesn't apply cleanly Mark Dixon (Fri Feb 27 2009 - 10:44:28 CST)
[AMBER] PLUMED release 1.0.0 available Massimiliano Bonomi (Thu Feb 26 2009 - 07:11:54 CST)
[AMBER] extra torsion terms in tleap.top-file Astrid Maaß (Thu Feb 26 2009 - 08:32:30 CST)
[AMBER] H-Bonds Beale, John (Thu Feb 26 2009 - 08:38:04 CST)
- Re: [AMBER] H-Bonds Thomas Cheatham III (Wed Mar 04 2009 - 15:00:30 CST)
  - [AMBER] What is the default position of the partial charges? Chih-Ying Lin (Wed Mar 04 2009 - 15:06:16 CST)
    - Re: [AMBER] What is the default position of the partial charges? Thomas Cheatham III (Wed Mar 04 2009 - 15:44:20 CST)
  - [AMBER] solvent and counter ions Taufik Al-Sarraj (Wed Mar 04 2009 - 15:36:36 CST)
[AMBER] (no subject) Lake, Thomas (Thu Feb 26 2009 - 10:19:53 CST)
- Re: [AMBER] (no subject) Carlos Simmerling (Thu Feb 26 2009 - 10:24:40 CST)
- [AMBER] MD simulations on a protein with FAD and NADH Mannan (Thu Feb 26 2009 - 19:11:54 CST)
  - RE: [AMBER] MD simulations on a protein with FAD and NADH Ross Walker (Thu Feb 26 2009 - 22:32:05 CST)
  - Re: [AMBER] MD simulations on a protein with FAD and NADH FyD (Fri Feb 27 2009 - 02:24:37 CST)
[AMBER] A problem with xleap and pdb file nancy4619 (Fri Feb 27 2009 - 06:28:01 CST)
- Re: [AMBER] A problem with xleap and pdb file David A. Case (Fri Feb 27 2009 - 07:56:26 CST)
  - Re:Re: [AMBER] A problem with xleap and pdb file nancy4619 (Fri Feb 27 2009 - 08:20:17 CST)
    - Re:Re: [AMBER] A problem with xleap and pdb file Peter Gannett (Fri Feb 27 2009 - 08:32:20 CST)
    - RE: Re: [AMBER] A problem with xleap and pdb file Ross Walker (Fri Feb 27 2009 - 09:55:23 CST)
[AMBER] Re: Antechamber kureeckal ramesh (Fri Feb 27 2009 - 06:56:58 CST)
- Re: [AMBER] Re: Antechamber FyD (Fri Feb 27 2009 - 07:12:16 CST)
  - Re:Re: [AMBER] Re: Antechamber null (Fri Feb 27 2009 - 08:00:07 CST)
[AMBER] I need a professional help about xleap and pdb file nancy4619 (Fri Feb 27 2009 - 07:56:14 CST)
- Re: [AMBER] I need a professional help about xleap and pdb file Peter Gannett (Fri Feb 27 2009 - 08:17:31 CST)
[AMBER] using Gromacs for analysis oguz gurbulak (Fri Feb 27 2009 - 11:03:54 CST)
- Re: [AMBER] using Gromacs for analysis Bala subramanian (Fri Feb 27 2009 - 12:16:46 CST)
- [AMBER] Re: using Gromacs for analysis oguz gurbulak (Mon Mar 02 2009 - 10:17:45 CST)
[AMBER] Partial entropy calculations ? Marek Malý (Fri Feb 27 2009 - 12:21:29 CST)
- Re: [AMBER] Partial entropy calculations ? Piotr Cieplak (Fri Feb 27 2009 - 12:44:21 CST)
[AMBER] PCL waleed zalloum (Sat Feb 28 2009 - 11:17:51 CST)
- RE: [AMBER] PCL Ross Walker (Sat Feb 28 2009 - 11:23:30 CST)
[AMBER] a query Molecular Dynamics (Sat Feb 28 2009 - 13:45:46 CST)
[AMBER] IMPORTANT INFO: Regarding Anonymous postings to the AMBER mailing list. Ross Walker (Sat Feb 28 2009 - 16:19:16 CST)
[AMBER] Question about NAB module Wei Huang (Sat Feb 28 2009 - 18:23:49 CST)
- Re: [AMBER] Question about NAB module David A. Case (Sun Mar 01 2009 - 07:52:19 CST)
  - RE: [AMBER] Question about NAB module Wei Huang (Sun Mar 01 2009 - 08:57:50 CST)
    - RE: [AMBER] Question about NAB module Andreas Svrcek-Seiler (Mon Mar 02 2009 - 03:23:52 CST)
[AMBER] binding free energy Maryam Hamzehee (Sun Mar 01 2009 - 05:52:43 CST)
- Re: [AMBER] binding free energy Barbault Florent (Sun Mar 01 2009 - 06:20:39 CST)
  - Re: [AMBER] binding free energy Don.Bashford_at_stjude.org (Sun Mar 01 2009 - 11:18:39 CST)
[AMBER] Pseudoatoms waleed zalloum (Mon Mar 02 2009 - 06:12:33 CST)
- Re: [AMBER] Pseudoatoms David A. Case (Mon Mar 02 2009 - 17:25:29 CST)
  - [AMBER] How to restart the umbrella sampling jobs? Catein Catherine (Mon Mar 02 2009 - 23:52:16 CST)
    - RE: [AMBER] How to restart the umbrella sampling jobs? Ross Walker (Tue Mar 03 2009 - 10:00:04 CST)
    - Re: [AMBER] How to restart the umbrella sampling jobs? Gustavo Seabra (Tue Mar 03 2009 - 14:41:25 CST)
[AMBER] How can I use the charge I calculated (using mol2 file) ? ÀÌÀ±°æ (Mon Mar 02 2009 - 07:27:39 CST)
- Re: [AMBER] How can I use the charge I calculated (using mol2 file) ? David A. Case (Mon Mar 02 2009 - 08:56:54 CST)
  - Re: Re: [AMBER] How can I use the charge I calculated (using mol2 file) ? ÀÌÀ±°æ (Mon Mar 02 2009 - 19:39:37 CST)
    - Re: Re: [AMBER] How can I use the charge I calculated (using mol2 file) ? David A. Case (Tue Mar 03 2009 - 07:39:26 CST)
    - Re: [AMBER] How can I use the charge I calculated (using mol2 file) ? FyD (Tue Mar 03 2009 - 08:12:18 CST)
[AMBER] calculate shear viscosity oguz gurbulak (Mon Mar 02 2009 - 07:35:06 CST)
[AMBER] assigning velocities to each atom without heating the system Parimal Kar (Mon Mar 02 2009 - 10:44:26 CST)
- Re: [AMBER] assigning velocities to each atom without heating the system Gustavo Seabra (Mon Mar 02 2009 - 11:31:09 CST)
  - Re: [AMBER] assigning velocities to each atom without heating the system Parimal Kar (Mon Mar 02 2009 - 11:46:25 CST)
- RE: [AMBER] assigning velocities to each atom without heating the system Ross Walker (Mon Mar 02 2009 - 14:23:22 CST)
[AMBER] specification of antechamber AC file format? Nicholas Musolino (Tue Mar 03 2009 - 01:53:23 CST)
- Re: [AMBER] specification of antechamber AC file format? David A. Case (Wed Mar 04 2009 - 16:39:44 CST)
[AMBER] inpcrd and prmtop m m (Tue Mar 03 2009 - 03:27:06 CST)
- Re: [AMBER] inpcrd and prmtop Hannes Loeffler (Tue Mar 03 2009 - 03:37:16 CST)
  - RE: [AMBER] inpcrd and prmtop m m (Tue Mar 03 2009 - 04:08:51 CST)
  - Re: [AMBER] inpcrd and prmtop FyD (Tue Mar 03 2009 - 04:19:43 CST)
- Re: [AMBER] inpcrd and prmtop Gustavo Seabra (Tue Mar 03 2009 - 14:20:38 CST)
[AMBER] Fail to allocate ff Madhurima Jana (Tue Mar 03 2009 - 05:17:57 CST)
- Re: [AMBER] Fail to allocate ff Nicholas Musolino (Tue Mar 03 2009 - 07:10:21 CST)
  - Re: [AMBER] Fail to allocate ff Madhurima Jana (Tue Mar 03 2009 - 08:27:41 CST)
- Re: [AMBER] Fail to allocate ff Gustavo Seabra (Tue Mar 03 2009 - 14:36:53 CST)
[AMBER] A good way to use an Amber force field with NAMD? Sasha Buzko (Tue Mar 03 2009 - 15:37:29 CST)
- Re: [AMBER] A good way to use an Amber force field with NAMD? Gustavo Seabra (Tue Mar 03 2009 - 18:08:33 CST)
  - Re: [AMBER] A good way to use an Amber force field with NAMD? Adrian Roitberg (Tue Mar 03 2009 - 18:11:49 CST)
[AMBER] Amber: water-water hydrogen bonding analysis on a subset of waters in a trajectory Jeff Schwinefus (Tue Mar 03 2009 - 16:18:25 CST)
- Re: [AMBER] Amber: water-water hydrogen bonding analysis on a subset of waters in a trajectory Thomas Cheatham III (Wed Mar 04 2009 - 13:59:30 CST)
  - Re: [AMBER] Amber: water-water hydrogen bonding analysis on a subset of waters in a trajectory Jeff Schwinefus (Wed Mar 04 2009 - 23:22:34 CST)
[AMBER] angle between ligand ring plane and axis Jia Xu (Wed Mar 04 2009 - 05:00:08 CST)
[AMBER] hydrogen bond . .. (Wed Mar 04 2009 - 05:12:33 CST)
- Re: [AMBER] hydrogen bond Carlos Simmerling (Wed Mar 04 2009 - 05:20:53 CST)
- RE: [AMBER] hydrogen bond Ross Walker (Wed Mar 04 2009 - 10:39:49 CST)
[AMBER] Regarding leap aneesh cna (Wed Mar 04 2009 - 05:43:52 CST)
- Re: [AMBER] Regarding leap Carlos Simmerling (Wed Mar 04 2009 - 05:48:30 CST)
- Re: [AMBER] Regarding leap Gustavo Seabra (Wed Mar 04 2009 - 16:05:25 CST)
  - Re: [AMBER] Regarding leap aneesh cna (Wed Mar 04 2009 - 22:29:17 CST)
    - Re: [AMBER] Regarding leap Gustavo Seabra (Thu Mar 05 2009 - 09:32:56 CST)
[AMBER] unning MMPBSA in CHCl3 environment SAFAK OZHAN (Wed Mar 04 2009 - 05:55:52 CST)
- Re: [AMBER] unning MMPBSA in CHCl3 environment Ray Luo (Wed Mar 04 2009 - 11:15:55 CST)
[AMBER] Thermodynamic Intergration problem Xiaohui Jiang [Contractor] (Wed Mar 04 2009 - 09:36:14 CST)
- RE: [AMBER] Thermodynamic Intergration problem Ross Walker (Wed Mar 04 2009 - 10:45:24 CST)
  - RE: [AMBER] Thermodynamic Intergration problem Xiaohui Jiang [Contractor] (Wed Mar 04 2009 - 11:00:06 CST)
[AMBER] Compilation and qmmm_div Benjamin Roberts (Wed Mar 04 2009 - 09:48:16 CST)
- RE: [AMBER] Compilation and qmmm_div Ross Walker (Wed Mar 04 2009 - 10:36:07 CST)
  - Re: [AMBER] Compilation and qmmm_div Benjamin Roberts (Wed Mar 04 2009 - 18:15:37 CST)
[AMBER] radial distribution function mask iccy liu (Wed Mar 04 2009 - 12:57:08 CST)
[AMBER] Segmentation faults Benjamin Roberts (Wed Mar 04 2009 - 18:17:50 CST)
Re: [AMBER] solvent and counter ions Bill Ross (Wed Mar 04 2009 - 18:20:45 CST)
[AMBER] DNA simulation: Problem with RMSD BERGY (Wed Mar 04 2009 - 21:44:26 CST)
- Re: [AMBER] DNA simulation: Problem with RMSD Thomas Cheatham (Wed Mar 04 2009 - 22:04:53 CST)
  - Re: [AMBER] DNA simulation: Problem with RMSD BERGY (Fri Mar 06 2009 - 00:20:00 CST)
[AMBER] Fwd: please help me out bharat lakhani (Wed Mar 04 2009 - 22:42:06 CST)
[AMBER] Re: Fw:How to creat .frcmod file FyD (Thu Mar 05 2009 - 00:22:56 CST)
[AMBER] please help me out bharat lakhani (Thu Mar 05 2009 - 02:35:44 CST)
- Re: [AMBER] please help me out FyD (Thu Mar 05 2009 - 03:22:20 CST)
  - Re: [AMBER] please help me out bharat lakhani (Thu Mar 05 2009 - 05:16:45 CST)
  - Re: [AMBER] please help me out bharat lakhani (Mon Mar 09 2009 - 00:04:45 CDT)
    - Re: [AMBER] please help me out FyD (Mon Mar 09 2009 - 03:10:08 CDT)
    - Re: [AMBER] please help me out bharat lakhani (Mon Mar 09 2009 - 03:43:08 CDT)
[AMBER] chemical shift penalty Jacopo Sgrignani (Thu Mar 05 2009 - 03:47:03 CST)
- Re: [AMBER] chemical shift penalty David A. Case (Thu Mar 05 2009 - 17:59:33 CST)
[AMBER] divcon error during antechamber run, convergence problem drugdesign (Thu Mar 05 2009 - 07:53:59 CST)
- Re: [AMBER] divcon error during antechamber run, convergence problem Martin Peters (Thu Mar 05 2009 - 08:21:19 CST)
- Re: [AMBER] divcon error during antechamber run, convergence problem Andrew Voronkov (Fri Mar 06 2009 - 12:04:55 CST)
  - Re: [AMBER] divcon error during antechamber run, convergence problem David A. Case (Fri Mar 06 2009 - 12:33:24 CST)
    - Re: [AMBER] divcon error during antechamber run, convergence problem Andrew Voronkov (Sat Mar 07 2009 - 09:58:19 CST)
[AMBER] secstruct Beale, John (Thu Mar 05 2009 - 07:54:20 CST)
- RE: [AMBER] secstruct Maxime Louet (Thu Feb 19 2009 - 08:17:17 CST)
  - Re: [AMBER] secstruct Carlos Simmerling (Thu Feb 19 2009 - 08:45:47 CST)
- Re: [AMBER] secstruct Carlos Simmerling (Thu Mar 05 2009 - 08:27:18 CST)
[AMBER] MM-PBSA decomp by residue and snapshot? Bradshaw, Richard (Thu Mar 05 2009 - 11:55:05 CST)
[AMBER] Warning: name change in pdb file residue Donald Keidel (Thu Mar 05 2009 - 13:25:38 CST)
- RE: [AMBER] Warning: name change in pdb file residue Duggan, Brendan M. (Thu Mar 05 2009 - 14:42:21 CST)
[AMBER] GBSA: dielectric symmetry Giacomo Bastianelli (Thu Mar 05 2009 - 17:29:50 CST)
- Re: [AMBER] GBSA: dielectric symmetry David A. Case (Thu Mar 05 2009 - 18:05:51 CST)
[AMBER] High RMSD for DNA: A to B transition study BERGY (Fri Mar 06 2009 - 01:26:57 CST)
- Re: [AMBER] High RMSD for DNA: A to B transition study David A. Case (Fri Mar 06 2009 - 08:57:02 CST)
  - Re: [AMBER] High RMSD for DNA: A to B transition study SENTHIL KUMAR (Fri Mar 13 2009 - 01:36:43 CDT)
    - Re: [AMBER] High RMSD for DNA: A to B transition study David A. Case (Fri Mar 13 2009 - 07:00:40 CDT)
[AMBER] Quality/size of HDD for Amber Francesco Pietra (Fri Mar 06 2009 - 03:26:03 CST)
- Re: [AMBER] Quality/size of HDD for Amber M. L. Dodson (Fri Mar 06 2009 - 09:44:45 CST)
  - Re: [AMBER] Quality/size of HDD for Amber Gustavo Seabra (Mon Mar 09 2009 - 12:44:54 CDT)
[AMBER] Solvate Box od amoeba water Hemant Gangwar (Fri Mar 06 2009 - 03:50:01 CST)
- Re: [AMBER] Solvate Box od amoeba water Wei Zhang (Fri Mar 06 2009 - 08:20:09 CST)
  - Re: [AMBER] Solvate Box od amoeba water Hemant Kumar (Sun Mar 22 2009 - 11:06:01 CDT)
[AMBER] catenan simulation problems Cristina Sisu (Fri Mar 06 2009 - 07:16:08 CST)
- Re: [AMBER] catenan simulation problems David A. Case (Fri Mar 06 2009 - 08:59:24 CST)
  - Re: [AMBER] catenan simulation problems Cristina Sisu (Fri Mar 06 2009 - 09:28:00 CST)
    - Re: [AMBER] catenan simulation problems David A. Case (Sat Mar 07 2009 - 17:25:07 CST)
    - Re: [AMBER] catenan simulation problems David A. Case (Wed Mar 18 2009 - 06:47:32 CDT)
  - Re: [AMBER] catenan simulation problems Cristina S.D. Sisu (Fri Mar 06 2009 - 09:35:46 CST)
[AMBER] Help with torsions in parm99.dat file Gregersen, Brent (Fri Mar 06 2009 - 16:44:17 CST)
- RE: [AMBER] Help with torsions in parm99.dat file Ross Walker (Fri Mar 06 2009 - 18:52:05 CST)
  - RE: [AMBER] Help with torsions in parm99.dat file Gregersen, Brent (Fri Mar 06 2009 - 20:15:11 CST)
    - RE: [AMBER] Help with torsions in parm99.dat file Ross Walker (Sat Mar 07 2009 - 00:32:23 CST)
  - Re: [AMBER] Help with torsions in parm99.dat file Astrid Maaß (Mon Mar 09 2009 - 08:27:30 CDT)
    - Re: [AMBER] Help with torsions in parm99.dat file Wei Zhang (Mon Mar 09 2009 - 09:38:56 CDT)
[AMBER] Problem with particle-mesh Ewald method Yunjie Zhao (Fri Mar 06 2009 - 21:29:02 CST)
- Re: [AMBER] Problem with particle-mesh Ewald method steinbrt_at_rci.rutgers.edu (Fri Mar 06 2009 - 21:42:26 CST)
- RE: [AMBER] Problem with particle-mesh Ewald method Ross Walker (Sat Mar 07 2009 - 00:10:34 CST)
[AMBER] analysis on Amber oguz gurbulak (Sat Mar 07 2009 - 12:04:19 CST)
- Re: [AMBER] analysis on Amber Thomas Cheatham (Sat Mar 07 2009 - 12:18:58 CST)
[AMBER] Fw:how to select force field Nancy (Sun Mar 08 2009 - 09:07:48 CDT)
- RE: [AMBER] Fw:how to select force field Ross Walker (Sun Mar 08 2009 - 12:52:56 CDT)
[AMBER] nmoldyn2 with Amber Adrien Delmont (Sun Mar 08 2009 - 09:37:40 CDT)
- Re: [AMBER] nmoldyn2 with Amber David Watson (Sun Mar 08 2009 - 09:54:57 CDT)
  - Re: [AMBER] nmoldyn2 with Amber M. L. Dodson (Sun Mar 08 2009 - 13:32:22 CDT)
    - Re: [AMBER] nmoldyn2 with Amber David Watson (Sun Mar 08 2009 - 15:00:39 CDT)
    - Re: [AMBER] nmoldyn2 with Amber Thomas Cheatham (Sun Mar 08 2009 - 15:10:17 CDT)
- Re: [AMBER] nmoldyn2 with Amber David Watson (Sun Mar 08 2009 - 10:02:55 CDT)
  - Re: [AMBER] nmoldyn2 with Amber M. L. Dodson (Sun Mar 08 2009 - 13:34:03 CDT)
[AMBER] addles segmentation fault gmail (Mon Mar 09 2009 - 03:28:56 CDT)
- Re: [AMBER] addles segmentation fault Carlos Simmerling (Mon Mar 09 2009 - 06:45:24 CDT)
  - Re: [AMBER] addles segmentation fault xiaonan zhang (Mon Mar 09 2009 - 08:08:47 CDT)
[AMBER] Particle-mesh Ewald method Yunjie Zhao (Mon Mar 09 2009 - 04:46:15 CDT)
- RE: [AMBER] Particle-mesh Ewald method Ross Walker (Mon Mar 09 2009 - 14:53:52 CDT)
[AMBER] 8Mureabox anna berteotti (Mon Mar 09 2009 - 05:07:52 CDT)
- Re: [AMBER] 8Mureabox David A. Case (Tue Mar 10 2009 - 07:51:08 CDT)
  - RE: [AMBER] 8Mureabox anna berteotti (Wed Mar 11 2009 - 03:45:03 CDT)
[AMBER] Restraint Mask length restriction !! Sampath Koppole (Mon Mar 09 2009 - 08:32:35 CDT)
- Re: [AMBER] Restraint Mask length restriction !! David A. Case (Mon Mar 09 2009 - 08:43:34 CDT)
- Re: [AMBER] Restraint Mask length restriction !! Sampath Koppole (Mon Mar 09 2009 - 09:06:23 CDT)
  - Re: [AMBER] Restraint Mask length restriction !! David A. Case (Mon Mar 09 2009 - 09:30:16 CDT)
- Re: [AMBER] Restraint Mask length restriction !! Sampath Koppole (Mon Mar 09 2009 - 09:39:38 CDT)
  - RE: [AMBER] Restraint Mask length restriction !! Ross Walker (Mon Mar 09 2009 - 14:50:08 CDT)
[AMBER] generalized distance restraint Rausch, Felix (Mon Mar 09 2009 - 08:48:01 CDT)
- Re: [AMBER] generalized distance restraint Carlos Simmerling (Mon Mar 09 2009 - 10:13:50 CDT)
  - RE: [AMBER] generalized distance restraint Rausch, Felix (Mon Mar 09 2009 - 11:15:11 CDT)
    - Re: [AMBER] generalized distance restraint Carlos Simmerling (Mon Mar 09 2009 - 11:39:43 CDT)
    - Re: [AMBER] generalized distance restraint M. L. Dodson (Mon Mar 09 2009 - 11:51:19 CDT)
- RE: [AMBER] generalized distance restraint Rausch, Felix (Wed Mar 11 2009 - 02:39:05 CDT)
[AMBER] Free Energy Decomposition Problem ozlem ulucan (Mon Mar 09 2009 - 08:55:45 CDT)
[AMBER] Changing Force Fields in "Midstream" Hopkins, Robert (Mon Mar 09 2009 - 19:12:27 CDT)
- RE: [AMBER] Changing Force Fields in "Midstream" Ross Walker (Mon Mar 09 2009 - 19:21:15 CDT)
  - RE: [AMBER] Changing Force Fields in "Midstream" Hopkins, Robert (Tue Mar 10 2009 - 18:29:44 CDT)
  - RE: [AMBER] Changing Force Fields in "Midstream" Hopkins, Robert (Wed Mar 11 2009 - 16:36:12 CDT)
[AMBER] problem in rmsd Parimal Kar (Mon Mar 09 2009 - 22:18:48 CDT)
- Re: [AMBER] problem in rmsd Thomas Cheatham (Mon Mar 09 2009 - 22:25:18 CDT)
  - Re: [AMBER] problem in rmsd Parimal Kar (Mon Mar 09 2009 - 22:36:13 CDT)
[AMBER] PB Bomb from MM-PBSA of Amber 10 Zhu, Yong-Liang (Mon Mar 09 2009 - 23:30:33 CDT)
- RE: [AMBER] PB Bomb from MM-PBSA of Amber 10 Wei Huang (Tue Mar 10 2009 - 05:30:50 CDT)
  - RE: [AMBER] PB Bomb from MM-PBSA of Amber 10 Zhu, Yong-Liang (Tue Mar 10 2009 - 11:06:43 CDT)
    - RE: [AMBER] PB Bomb from MM-PBSA of Amber 10 Wei Huang (Tue Mar 10 2009 - 11:20:29 CDT)
- RE: [AMBER] PB Bomb from MM-PBSA of Amber 10 Ray Luo (Tue Mar 10 2009 - 11:28:15 CDT)
[AMBER] sulfotyrosine parameters Ryan Pavlovicz (Tue Mar 10 2009 - 10:05:59 CDT)
[AMBER] wrong estimation of hydrogen velocities when using SHAKE? Jose Borreguero (Tue Mar 10 2009 - 11:09:48 CDT)
- Re: [AMBER] wrong estimation of hydrogen velocities when using SHAKE? David A. Case (Wed Mar 11 2009 - 06:08:17 CDT)
  - Re: [AMBER] wrong estimation of hydrogen velocities when using SHAKE? Jose Borreguero (Wed Mar 11 2009 - 12:28:21 CDT)
[AMBER] about MD simulation ÁÎÇà»ª (Wed Mar 11 2009 - 04:19:28 CDT)
- Re: [AMBER] about MD simulation Carlos Simmerling (Wed Mar 11 2009 - 05:56:43 CDT)
  - å›žå¤ï¼š [AMBER] about MD simulation å»–é’åŽ (Wed Mar 11 2009 - 11:25:05 CDT)
[AMBER] Seeking for suggestion related to plot the cluster out file S.Sundar Raman (Wed Mar 11 2009 - 07:44:17 CDT)
- RE: [AMBER] Seeking for suggestion related to plot the cluster out file Ross Walker (Wed Mar 11 2009 - 09:33:38 CDT)
  - Re: [AMBER] Seeking for suggestion related to plot the cluster out file S.Sundar Raman (Wed Mar 11 2009 - 09:57:40 CDT)
    - RE: [AMBER] Seeking for suggestion related to plot the cluster out file Ross Walker (Wed Mar 11 2009 - 10:55:38 CDT)
    - Re: [AMBER] Seeking for suggestion related to plot the cluster out file S.Sundar Raman (Wed Mar 11 2009 - 11:07:25 CDT)
[AMBER] installing AmberTools on Windows machines David A. Case (Wed Mar 11 2009 - 15:27:07 CDT)
[AMBER] polarizable force field and solvent zeinab bagheri (Wed Mar 11 2009 - 17:02:06 CDT)
[AMBER] Understanding the all.out file in the MM-PBSA output gmail (Wed Mar 11 2009 - 20:39:10 CDT)
- Re: [AMBER] Understanding the all.out file in the MM-PBSA output Hannes Kopitz (Thu Mar 12 2009 - 05:54:27 CDT)
  - RE: [AMBER] Understanding the all.out file in the MM-PBSA output Ray Luo (Thu Mar 12 2009 - 11:29:22 CDT)
[AMBER] polarizable force field and solvent zeinab bagheri (Thu Mar 12 2009 - 00:40:33 CDT)
[AMBER] Problem with REMD parul sharma (Thu Mar 12 2009 - 02:45:09 CDT)
- Re: [AMBER] Problem with REMD Carlos Simmerling (Thu Mar 12 2009 - 06:00:07 CDT)
[AMBER] Problems with MM-PBSA Calculation after MD German Erlenkamp (Thu Mar 12 2009 - 04:28:23 CDT)
- Re: [AMBER] Problems with MM-PBSA Calculation after MD Hannes Kopitz (Thu Mar 12 2009 - 06:06:54 CDT)
[AMBER] SMD in Amber10 Dmitri Nilov (Thu Mar 12 2009 - 13:12:13 CDT)
- Re: [AMBER] SMD in Amber10 Adrian Roitberg (Thu Mar 12 2009 - 13:46:14 CDT)
  - Re: [AMBER] SMD in Amber10 Dmitri Nilov (Fri Mar 13 2009 - 03:52:26 CDT)
[AMBER] Thermodynamic Integration at higher values of clambda using AMBER 9 PRADEEP VENKATARAMAN (Thu Mar 12 2009 - 16:56:59 CDT)
- Re: [AMBER] Thermodynamic Integration at higher values of clambda using AMBER 9 steinbrt_at_rci.rutgers.edu (Thu Mar 12 2009 - 19:37:08 CDT)
[AMBER] Problem running test.pmemd.AMOEBA mloureiro_at_cesga.es (Fri Mar 13 2009 - 06:45:30 CDT)
- [AMBER] Problem build pmemd Yiannis Georgiadis (Fri Mar 13 2009 - 19:14:49 CDT)
  - Re: [AMBER] Problem build pmemd Robert Duke (Fri Mar 13 2009 - 07:40:09 CDT)
  - Re: [AMBER] Problem build pmemd Atro Tossavainen (Sat Mar 14 2009 - 14:10:53 CDT)
- Re: [AMBER] Problem running test.pmemd.AMOEBA Robert Duke (Fri Mar 13 2009 - 09:33:55 CDT)
[AMBER] to understand multiplicity in antechamber Alan (Fri Mar 13 2009 - 07:06:45 CDT)
[AMBER] to understand multiplicity in antechamber Alan (Fri Mar 13 2009 - 09:43:45 CDT)
- Re: [AMBER] to understand multiplicity in antechamber Scott Brozell (Fri Mar 13 2009 - 14:05:06 CDT)
  - Re: [AMBER] to understand multiplicity in antechamber Alan (Fri Mar 13 2009 - 17:43:28 CDT)
[AMBER] doubt-reg_ Targeted molecular dynamics balaji nagarajan (Fri Mar 13 2009 - 11:20:41 CDT)
[AMBER] problems compiling ambertool Per Jr. Greisen (Fri Mar 13 2009 - 14:08:36 CDT)
- Re: [AMBER] problems compiling ambertool David A. Case (Fri Mar 13 2009 - 14:54:56 CDT)
- Re: [AMBER] problems compiling ambertool Bill Ross (Mon Mar 16 2009 - 17:50:44 CDT)
  - Re: [AMBER] problems compiling ambertool Per Jr. Greisen (Tue Mar 17 2009 - 03:10:20 CDT)
- Re: [AMBER] problems compiling ambertool Bill Ross (Tue Mar 17 2009 - 12:10:01 CDT)
- Re: [AMBER] problems compiling ambertool Bill Ross (Tue Mar 17 2009 - 12:24:48 CDT)
  - Re: [AMBER] problems compiling ambertool Per Jr. Greisen (Wed Mar 18 2009 - 06:49:57 CDT)
[AMBER] suggestions for PB simulation Bala subramanian (Sat Mar 14 2009 - 11:41:19 CDT)
[AMBER] sander.MPI and pmemd.MPI in Fedora 8 John Bennett (Sun Mar 15 2009 - 16:23:16 CDT)
[AMBER] Unit 5 Error on OPEN: nan.in Nancy (Mon Mar 16 2009 - 07:49:31 CDT)
[AMBER] about mm-pbsa å»–é’åŽ (Mon Mar 16 2009 - 09:59:40 CDT)
[AMBER] about mm-pbsa å»–é’åŽ (Mon Mar 16 2009 - 10:02:49 CDT)
- RE: [AMBER] about mm-pbsa Wei Huang (Mon Mar 16 2009 - 10:17:30 CDT)
[AMBER] minimisation with igb=10 Bala subramanian (Mon Mar 16 2009 - 10:43:10 CDT)
- Re: [AMBER] minimisation with igb=10 Carlos Simmerling (Mon Mar 16 2009 - 10:45:47 CDT)
  - Re: [AMBER] minimisation with igb=10 Bala subramanian (Mon Mar 16 2009 - 10:56:48 CDT)
    - Re: [AMBER] minimisation with igb=10 Carlos Simmerling (Mon Mar 16 2009 - 11:04:37 CDT)
    - RE: [AMBER] minimisation with igb=10 Ray Luo (Mon Mar 16 2009 - 11:34:21 CDT)
[AMBER] Actual force constant in SMD Dmitri Nilov (Mon Mar 16 2009 - 13:07:09 CDT)
[AMBER] Re: join two units in amber9 or amber10 Taufik Al-Sarraj (Mon Mar 16 2009 - 16:11:30 CDT)
Re: [AMBER] Re: join two units in amber9 or amber10 Bill Ross (Mon Mar 16 2009 - 17:56:01 CDT)
[AMBER] Unit 5 Error on OPEN: nan.in Nancy (Mon Mar 16 2009 - 20:02:09 CDT)
[AMBER] Input file of the second stage RESP fitting Cen Gao (Mon Mar 16 2009 - 23:29:17 CDT)
- Re: [AMBER] Input file of the second stage RESP fitting FyD (Tue Mar 17 2009 - 08:32:58 CDT)
  - Re: [AMBER] Input file of the second stage RESP fitting Cen Gao (Tue Mar 17 2009 - 16:24:24 CDT)
[AMBER] regarding tutorial on united atom force field jani sahil (Mon Mar 16 2009 - 23:51:16 CDT)
- Re: [AMBER] regarding tutorial on united atom force field Ray Luo (Tue Mar 17 2009 - 11:22:01 CDT)
[AMBER] need- help-for TMD balaji nagarajan (Tue Mar 17 2009 - 00:16:34 CDT)
[AMBER] Unit 5 Error on OPEN: nan.in Nancy (Tue Mar 17 2009 - 04:11:10 CDT)
- Re: [AMBER] Unit 5 Error on OPEN: nan.in mathew k varghese (Mon Mar 16 2009 - 08:36:57 CDT)
  - Re:Re: [AMBER] Unit 5 Error on OPEN: nan.in Nancy (Mon Mar 16 2009 - 09:01:14 CDT)
    - Re: Re: [AMBER] Unit 5 Error on OPEN: nan.in Carlos Simmerling (Mon Mar 16 2009 - 09:32:02 CDT)
- Re: [AMBER] Unit 5 Error on OPEN: nan.in mathew k varghese (Tue Mar 17 2009 - 06:22:08 CDT)
  - Re: [AMBER] Unit 5 Error on OPEN: nan.in Jenny Iskrenova (Tue Mar 17 2009 - 07:34:00 CDT)
  - Re:Re: [AMBER] Unit 5 Error on OPEN: nan.in Nancy (Tue Mar 17 2009 - 08:37:44 CDT)
[AMBER] removing center of mass Bala subramanian (Tue Mar 17 2009 - 10:21:28 CDT)
[AMBER] convert .mol2 file to .pdb with atomtype definitions Pansy Patel (Tue Mar 17 2009 - 10:50:57 CDT)
- Re: [AMBER] convert .mol2 file to .pdb with atomtype definitions David A. Case (Tue Mar 17 2009 - 11:00:19 CDT)
  - Re: [AMBER] convert .mol2 file to .pdb with atomtype definitions Pansy Patel (Tue Mar 17 2009 - 11:09:10 CDT)
    - Re: [AMBER] convert .mol2 file to .pdb with atomtype definitions Wei Zhang (Tue Mar 17 2009 - 11:33:27 CDT)
    - RE: [AMBER] convert .mol2 file to .pdb with atomtype definitions Pankaj R. Daga (Tue Mar 17 2009 - 11:41:20 CDT)
[AMBER] temperature rises with igb=1 Bala subramanian (Tue Mar 17 2009 - 11:35:41 CDT)
- Re: [AMBER] temperature rises with igb=1 Carlos Simmerling (Tue Mar 17 2009 - 11:44:32 CDT)
- RE: [AMBER] temperature rises with igb=1 Ross Walker (Tue Mar 17 2009 - 11:53:04 CDT)
  - Re: [AMBER] temperature rises with igb=1 Carlos Simmerling (Tue Mar 17 2009 - 11:58:05 CDT)
    - Re: [AMBER] temperature rises with igb=1 Bala subramanian (Thu Mar 19 2009 - 06:24:45 CDT)
    - Re: [AMBER] temperature rises with igb=1 David A. Case (Thu Mar 19 2009 - 07:04:54 CDT)
Re: [AMBER] Unit 5 Error on OPEN: nan.in Bill Ross (Tue Mar 17 2009 - 12:12:07 CDT)
[AMBER] CCL4 simulation sudipta (Tue Mar 17 2009 - 13:18:07 CDT)
- Re: [AMBER] CCL4 simulation David A. Case (Tue Mar 17 2009 - 21:14:51 CDT)
  - Re: [AMBER] CCL4 simulation sudipta (Wed Mar 18 2009 - 02:47:48 CDT)
    - Re: [AMBER] CCL4 simulation David A. Case (Wed Mar 18 2009 - 06:06:30 CDT)
[AMBER] error in constructing DNA from nucgen Pansy Patel (Tue Mar 17 2009 - 13:43:49 CDT)
- Re: [AMBER] error in constructing DNA from nucgen Carlos Simmerling (Tue Mar 17 2009 - 13:53:05 CDT)
  - Re: [AMBER] error in constructing DNA from nucgen Pansy Patel (Tue Mar 17 2009 - 14:24:58 CDT)
    - RE: [AMBER] error in constructing DNA from nucgen Ross Walker (Tue Mar 17 2009 - 14:31:16 CDT)
- Re: [AMBER] error in constructing DNA from nucgen Carlos Simmerling (Tue Mar 17 2009 - 13:53:05 CDT)
- Re: [AMBER] error in constructing DNA from nucgen Carlos Simmerling (Tue Mar 17 2009 - 13:53:05 CDT)
- Re: [AMBER] error in constructing DNA from nucgen Bill Ross (Tue Mar 17 2009 - 17:47:07 CDT)
[AMBER] TMD balaji nagarajan (Tue Mar 17 2009 - 23:58:37 CDT)
- Re: [AMBER] TMD Carlos Simmerling (Wed Mar 18 2009 - 05:32:14 CDT)
  - RE: [AMBER] TMD balaji nagarajan (Wed Mar 18 2009 - 06:15:55 CDT)
[AMBER] About error of "vertex atom mismatch" å»–é’åŽ (Wed Mar 18 2009 - 03:30:29 CDT)
[AMBER] errors about install amber9 on MAC OS zgong.hust (Wed Mar 18 2009 - 03:41:19 CDT)
- Re: [AMBER] errors about install amber9 on MAC OS David A. Case (Wed Mar 18 2009 - 06:08:44 CDT)
[AMBER] protein protrudes from unit cell Jeffrey (Wed Mar 18 2009 - 03:59:06 CDT)
- Re: [AMBER] protein protrudes from unit cell Hannes Loeffler (Wed Mar 18 2009 - 04:08:41 CDT)
- RE: [AMBER] protein protrudes from unit cell Ross Walker (Wed Mar 18 2009 - 10:39:23 CDT)
  - Re: [AMBER] protein protrudes from unit cell Carlos Simmerling (Wed Mar 18 2009 - 10:49:43 CDT)
[AMBER] sleap and check Alan (Wed Mar 18 2009 - 06:18:27 CDT)
- Re: [AMBER] sleap and check Wei Zhang (Wed Mar 18 2009 - 09:40:57 CDT)
  - Re: [AMBER] sleap and check Alan (Wed Mar 18 2009 - 16:23:51 CDT)
[AMBER] Mass of LP PRADEEP VENKATARAMAN (Wed Mar 18 2009 - 22:27:24 CDT)
- Re: [AMBER] Mass of LP David A. Case (Thu Mar 19 2009 - 06:27:48 CDT)
[AMBER] simulation in water-oil (or water/hydrophobic-solvent) box ranga nath (Wed Mar 18 2009 - 23:27:54 CDT)
- Re: [AMBER] simulation in water-oil (or water/hydrophobic-solvent) box David A. Case (Thu Mar 19 2009 - 12:38:52 CDT)
  - [AMBER] protein PDB Chih-Ying Lin (Thu Mar 19 2009 - 15:43:15 CDT)
  - Re: [AMBER] simulation in water-oil (or water/hydrophobic-solvent) box ranga nath (Sat Mar 21 2009 - 21:04:13 CDT)
[AMBER] Metal in MD simulation priya priya (Thu Mar 19 2009 - 01:25:09 CDT)
- Re: [AMBER] Metal in MD simulation Jagadeesh, M.N., Ph.D. (Thu Mar 19 2009 - 09:48:28 CDT)
- RE: [AMBER] Metal in MD simulation Ross Walker (Thu Mar 19 2009 - 10:12:24 CDT)
- Re: [AMBER] Metal in MD simulation Bill Ross (Thu Mar 19 2009 - 16:22:12 CDT)
- Re: [AMBER] Metal in MD simulation priya priya (Fri Mar 20 2009 - 01:15:06 CDT)
[AMBER] About mm-pbsa å»–é’åŽ (Thu Mar 19 2009 - 01:48:21 CDT)
[AMBER] [about advanced tutorial 1] How could I get conformations for gaussian that have minimum energy? Youn Kyeung Lee (Thu Mar 19 2009 - 02:31:16 CDT)
- Re: [AMBER] [about advanced tutorial 1] How could I get conformations for gaussian that have minimum energy? FyD (Sun Mar 22 2009 - 15:12:17 CDT)
[AMBER] error for nmode Dechang Li (Thu Mar 19 2009 - 06:00:09 CDT)
- Re: [AMBER] error for nmode David A. Case (Thu Mar 19 2009 - 06:31:24 CDT)
[AMBER] pmemd compile error.... Giorgos Lamprinidis (Thu Mar 19 2009 - 10:06:04 CDT)
- Re: [AMBER] pmemd compile error.... Robert Duke (Thu Mar 19 2009 - 10:24:29 CDT)
  - Re: [AMBER] pmemd compile error.... Yiannis Georgiadis (Tue Mar 24 2009 - 15:10:27 CDT)
    - Re: [AMBER] pmemd compile error.... case (Tue Mar 24 2009 - 07:12:46 CDT)
    - Re: [AMBER] pmemd compile error.... Robert Duke (Tue Mar 24 2009 - 07:19:45 CDT)
- Re: [AMBER] pmemd compile error.... Robert Duke (Thu Mar 19 2009 - 10:25:04 CDT)
[AMBER] Parametrisation of Silicon based molecules for Amber simulations ? Marek Malý (Thu Mar 19 2009 - 18:49:21 CDT)
- [AMBER] FF Parameters Transformations ...? Marek Malý (Wed Apr 01 2009 - 12:29:26 CDT)
  - Re: [AMBER] FF Parameters Transformations ...? Karl Kirschner (Mon Apr 06 2009 - 02:39:31 CDT)
    - Re: [AMBER] FF Parameters Transformations ...? Marek Malý (Mon Apr 06 2009 - 15:03:58 CDT)
[AMBER] analysing DNA trajectory balaji nagarajan (Fri Mar 20 2009 - 00:09:10 CDT)
- Re: [AMBER] analysing DNA trajectory Bala subramanian (Fri Mar 20 2009 - 03:06:08 CDT)
[AMBER] Help needed in amber parallel installation sushobhan_at_iiar.res.in (Fri Mar 20 2009 - 01:39:36 CDT)
- Re: [AMBER] Help needed in amber parallel installation Carlos Simmerling (Fri Mar 20 2009 - 06:34:31 CDT)
- RE: [AMBER] Help needed in amber parallel installation Ross Walker (Fri Mar 20 2009 - 10:40:30 CDT)
[AMBER] QM/MM charges Jacopo Sgrignani (Fri Mar 20 2009 - 04:38:30 CDT)
- RE: [AMBER] QM/MM charges Ross Walker (Fri Mar 20 2009 - 10:37:34 CDT)
[AMBER] Announcement of Model(l)ing'09 - The annual 2009 MGMS Meeting in Erlangen, Germany Harald Lanig (Fri Mar 20 2009 - 06:25:09 CDT)
[AMBER] MMGBSA IG Value Rajesh Raju (Fri Mar 20 2009 - 12:20:52 CDT)
- Re: [AMBER] MMGBSA IG Value Carlos Simmerling (Fri Mar 20 2009 - 12:25:38 CDT)
  - Re: [AMBER] MMGBSA IG Value Rajesh Raju (Fri Mar 20 2009 - 12:36:37 CDT)
    - Re: [AMBER] MMGBSA IG Value Carlos Simmerling (Fri Mar 20 2009 - 12:42:14 CDT)
[AMBER] xmgrace Nancy (Fri Mar 20 2009 - 23:41:33 CDT)
- Re: [AMBER] xmgrace mathew k varghese (Sat Mar 21 2009 - 00:18:32 CDT)
  - Re:Re: [AMBER] xmgrace Nancy (Sat Mar 21 2009 - 00:42:48 CDT)
[AMBER] adding chain id to ptraj pdb output Paul Brandt (Sat Mar 21 2009 - 21:09:59 CDT)
- Re: [AMBER] adding chain id to ptraj pdb output Bala subramanian (Mon Mar 23 2009 - 06:37:43 CDT)
- Re: [AMBER] adding chain id to ptraj pdb output Joe Krahn (Mon Mar 23 2009 - 18:20:30 CDT)
[AMBER] about mm-pbsa å»–é’åŽ (Mon Mar 23 2009 - 04:10:29 CDT)
[AMBER] leap and chirality Karl Kirschner (Mon Mar 23 2009 - 04:54:29 CDT)
- Re: [AMBER] leap and chirality David A. Case (Mon Mar 23 2009 - 08:16:14 CDT)
  - Re: [AMBER] leap and chirality Karl Kirschner (Mon Mar 23 2009 - 09:05:56 CDT)
[AMBER] problem in installing AMBER10 Dr. Debaprasad Giri (Mon Mar 23 2009 - 05:31:26 CDT)
- Re: [AMBER] problem in installing AMBER10 David A. Case (Mon Mar 23 2009 - 06:07:17 CDT)
  - Re: [AMBER] problem in installing AMBER10 Dr. Debaprasad Giri (Fri Mar 27 2009 - 05:16:47 CDT)
    - Re: [AMBER] problem in installing AMBER10 David A. Case (Fri Mar 27 2009 - 07:05:31 CDT)
    - Re: [AMBER] problem in installing AMBER10 Dr. Debaprasad Giri (Sat Apr 04 2009 - 07:13:46 CDT)
[AMBER] Regarding use of PME along with Implict solvation jani sahil (Mon Mar 23 2009 - 05:38:39 CDT)
- Re: [AMBER] Regarding use of PME along with Implict solvation parul sharma (Mon Mar 23 2009 - 05:55:24 CDT)
  - Re: [AMBER] Regarding use of PME along with Implict solvation jani sahil (Mon Mar 23 2009 - 08:04:15 CDT)
[AMBER] helical parameters balaji nagarajan (Mon Mar 23 2009 - 11:21:04 CDT)
- Re: [AMBER] helical parameters Bala subramanian (Mon Mar 23 2009 - 13:14:29 CDT)
[AMBER] pmemd compile error Giorgos Lamprinidis (Mon Mar 23 2009 - 15:54:37 CDT)
- Re: [AMBER] pmemd compile error Robert Duke (Mon Mar 23 2009 - 16:03:45 CDT)
[AMBER] errors on reading time series file in WHAM calculation gmail (Mon Mar 23 2009 - 19:35:02 CDT)
- Re: [AMBER] errors on reading time series file in WHAM calculation Jenny Iskrenova (Tue Mar 24 2009 - 09:35:51 CDT)
[AMBER] validation of parameters and request of suggestions Jeffrey (Mon Mar 23 2009 - 21:16:35 CDT)
[AMBER] continuam water Mannan (Mon Mar 23 2009 - 23:11:50 CDT)
- Re: [AMBER] continuam water Carlos Simmerling (Tue Mar 24 2009 - 08:36:15 CDT)
  - [AMBER] POLARIZABLE WATER MODEL CHAMI F. (Tue Mar 24 2009 - 13:03:25 CDT)
[AMBER] change in protein ligand order Hannes Wallnoefer (Tue Mar 24 2009 - 06:05:36 CDT)
- Re: [AMBER] change in protein ligand order Hannes Loeffler (Tue Mar 24 2009 - 06:27:24 CDT)
  - Re: [AMBER] change in protein ligand order Hannes Wallnoefer (Tue Mar 24 2009 - 07:38:18 CDT)
- Re: [AMBER] change in protein ligand order Bill Ross (Tue Mar 24 2009 - 13:07:42 CDT)
  - Re: [AMBER] change in protein ligand order Hannes Wallnoefer (Tue Mar 24 2009 - 15:45:16 CDT)
[AMBER] validation of parameters and request suggestions Jeffrey (Tue Mar 24 2009 - 06:52:19 CDT)
[AMBER] create new crd files from transformed coordinates Donald Keidel (Tue Mar 24 2009 - 20:49:03 CDT)
- Re: [AMBER] create new crd files from transformed coordinates case (Wed Mar 25 2009 - 07:26:29 CDT)
[AMBER] question about pair wise per-residue energy decomposition; idecomp=3 wfli_at_biophy.nju.edu.cn (Wed Mar 25 2009 - 04:48:29 CDT)
- Re: [AMBER] question about pair wise per-residue energy decomposition; idecomp=3 case (Wed Mar 25 2009 - 13:58:02 CDT)
[AMBER] About Free energy decomposition Rajesh Raju (Wed Mar 25 2009 - 09:08:00 CDT)
[AMBER] Rosetta Academic Training Webinar Nir London (Wed Mar 25 2009 - 11:14:21 CDT)
[AMBER] How to reproduce a parallel PMEMD run? Siang Yip (Wed Mar 25 2009 - 17:33:56 CDT)
- Re: [AMBER] How to reproduce a parallel PMEMD run? Robert Duke (Wed Mar 25 2009 - 18:45:49 CDT)
[AMBER] Amber 10 and core i7 Supat Jiranusornkul (Thu Mar 26 2009 - 04:13:10 CDT)
[AMBER] To find radial distribution curve nicholus bhattacharjee (Thu Mar 26 2009 - 12:16:07 CDT)
[AMBER] installing resp on linux 64bit aditya chhikara (Thu Mar 26 2009 - 12:24:27 CDT)
- Re: [AMBER] installing resp on linux 64bit FyD (Thu Mar 26 2009 - 14:37:22 CDT)
  - Re: [AMBER] installing resp on linux 64bit aditya chhikara (Thu Mar 26 2009 - 16:36:50 CDT)
[AMBER] Problem with "Atom does not have a type" Richard Tseng (Thu Mar 26 2009 - 18:17:19 CDT)
- Re: [AMBER] Problem with "Atom does not have a type" David A. Case (Fri Mar 27 2009 - 06:44:22 CDT)
  - Re: [AMBER] Problem with "Atom does not have a type" Richard Tseng (Fri Mar 27 2009 - 16:51:32 CDT)
[AMBER] Fwd: AMBER: MM-PBSA in AMBER 10 Daniel Oehme (Thu Mar 26 2009 - 18:44:59 CDT)
- Re: [AMBER] Fwd: AMBER: MM-PBSA in AMBER 10 Ray Luo (Thu Mar 26 2009 - 18:54:17 CDT)
[AMBER] Problem reading PDB file into XLEAP Hopkins, Robert (Thu Mar 26 2009 - 19:01:26 CDT)
- Re: [AMBER] Problem reading PDB file into XLEAP David A. Case (Fri Mar 27 2009 - 07:39:26 CDT)
  - RE: [AMBER] Problem reading PDB file into XLEAP Hopkins, Robert (Fri Mar 27 2009 - 17:09:11 CDT)
[AMBER] Antechamber problem Å·ÑôµÂ·½ (Thu Mar 26 2009 - 23:44:24 CDT)
- Re: [AMBER] Antechamber problem David A. Case (Fri Mar 27 2009 - 07:29:48 CDT)
- Re: [AMBER] Antechamber problem Junmei Wang (Fri Mar 27 2009 - 16:21:33 CDT)
  - RE: [AMBER] Antechamber problem Å·ÑôµÂ·½ (Fri Mar 27 2009 - 19:55:03 CDT)
[AMBER] problem using amoeba Hemant Gangwar (Fri Mar 27 2009 - 05:41:26 CDT)
- Re: [AMBER] problem using amoeba Robert Duke (Fri Mar 27 2009 - 07:22:31 CDT)
[AMBER] Question Kshatresh Dutta Dubey (Fri Mar 27 2009 - 08:06:09 CDT)
- RE: [AMBER] Question Rausch, Felix (Fri Mar 27 2009 - 08:37:29 CDT)
  - Re: [AMBER] Question Kshatresh Dutta Dubey (Sat Mar 28 2009 - 04:16:03 CDT)
    - Re: [AMBER] Question David A. Case (Sat Mar 28 2009 - 08:38:49 CDT)
- [AMBER] BINDER/xaLeap Taufik Al-Sarraj (Mon Mar 30 2009 - 20:00:10 CDT)
  - RE: [AMBER] BINDER/xaLeap Ross Walker (Mon Mar 30 2009 - 20:29:46 CDT)
[AMBER] PMEMD 9 on MVAPICH / Infiniband problem Nick Holway (Fri Mar 27 2009 - 10:55:38 CDT)
- RE: [AMBER] PMEMD 9 on MVAPICH / Infiniband problem Ross Walker (Fri Mar 27 2009 - 20:04:04 CDT)
  - Re: [AMBER] PMEMD 9 on MVAPICH / Infiniband problem fohm fohm (Tue Mar 31 2009 - 06:04:10 CDT)
    - Re: [AMBER] PMEMD 9 on MVAPICH / Infiniband problem Robert Duke (Tue Mar 31 2009 - 07:21:22 CDT)
[AMBER] Load protein complex to Xleap (Combine) Rilei Yu (Fri Mar 27 2009 - 21:30:04 CDT)
- Re: [AMBER] Load protein complex to Xleap (Combine) David A. Case (Sat Mar 28 2009 - 16:39:35 CDT)
- Re: [AMBER] Load protein complex to Xleap (Combine) Rilei Yu (Sat Mar 28 2009 - 20:17:21 CDT)
  - Re: [AMBER] Load protein complex to Xleap (Combine) David A. Case (Sat Mar 28 2009 - 21:26:58 CDT)
- Re: [AMBER] Load protein complex to Xleap (Combine) Rilei Yu (Sat Mar 28 2009 - 22:07:47 CDT)
- Re: [AMBER] Load protein complex to Xleap (Combine) Rilei Yu (Sat Mar 28 2009 - 23:00:00 CDT)
  - Re: [AMBER] Load protein complex to Xleap (Combine) David A. Case (Sun Mar 29 2009 - 13:41:13 CDT)
[AMBER] .rst file generation problem. Aravind S (Mon Mar 30 2009 - 00:48:55 CDT)
- Re: [AMBER] .rst file generation problem. Aravind S (Mon Mar 30 2009 - 01:32:12 CDT)
- Re: [AMBER] .rst file generation problem. Carlos Simmerling (Mon Mar 30 2009 - 06:30:58 CDT)
- Re: [AMBER] .rst file generation problem. Aravind S (Tue Mar 31 2009 - 03:49:17 CDT)
  - Re: [AMBER] .rst file generation problem. Carlos Simmerling (Tue Mar 31 2009 - 06:28:35 CDT)
[AMBER] "rfree: End of file on unit 5" Remya S R (Mon Mar 30 2009 - 01:21:53 CDT)
- Re: [AMBER] "rfree: End of file on unit 5" mathew k varghese (Mon Mar 30 2009 - 04:57:44 CDT)
[AMBER] mm_pbsa problem Giorgos Lamprinidis (Mon Mar 30 2009 - 05:02:07 CDT)
- Re: [AMBER] mm_pbsa problem case (Mon Mar 30 2009 - 07:48:05 CDT)
  - Re: [AMBER] mm_pbsa problem Giorgos Lamprinidis (Mon Mar 30 2009 - 08:59:55 CDT)
    - RE: [AMBER] mm_pbsa problem Ray Luo (Mon Mar 30 2009 - 12:27:59 CDT)
    - Re: [AMBER] mm_pbsa problem Giorgos Lamprinidis (Wed Apr 01 2009 - 02:36:53 CDT)
[AMBER] Creating conditions for biased MD Francesco Pietra (Mon Mar 30 2009 - 05:16:54 CDT)
- Re: [AMBER] Creating conditions for biased MD Carlos Simmerling (Mon Mar 30 2009 - 06:56:36 CDT)
  - Re: [AMBER] Creating conditions for biased MD Francesco Pietra (Mon Apr 20 2009 - 12:31:52 CDT)
- Re: [AMBER] Creating conditions for biased MD Bill Ross (Wed Apr 22 2009 - 11:19:20 CDT)
  - Re: [AMBER] Creating conditions for biased MD Francesco Pietra (Wed Apr 22 2009 - 13:01:39 CDT)
[AMBER] amber tools installation Jayalakshmi Sridhar (Mon Mar 30 2009 - 10:44:57 CDT)
- Re: [AMBER] amber tools installation case (Mon Mar 30 2009 - 11:28:38 CDT)
[AMBER] Announcing NMR validation web interface iCing Alan (Mon Mar 30 2009 - 11:55:00 CDT)
[AMBER] problem with the results in the .out file! Aravind S (Tue Mar 31 2009 - 00:30:57 CDT)
- Re: [AMBER] problem with the results in the .out file! Gustavo Seabra (Tue Mar 31 2009 - 08:01:41 CDT)
  - Re: [AMBER] problem with the results in the .out file! Aravind S (Thu Apr 02 2009 - 00:49:19 CDT)
[AMBER] how to convert secstruct output file into plot or pictorial representation Siddharth Rastogi (Tue Mar 31 2009 - 05:56:37 CDT)
[AMBER] modifying LYN Marius Retegan (Tue Mar 31 2009 - 08:36:21 CDT)
- Re: [AMBER] modifying LYN FyD (Tue Mar 31 2009 - 10:41:56 CDT)
  - Re: [AMBER] modifying LYN Marius Retegan (Tue Mar 31 2009 - 11:58:06 CDT)
[AMBER] combine many coord files into trajectory file Peter Gannett (Tue Mar 31 2009 - 08:51:16 CDT)
- Re: [AMBER] combine many coord files into trajectory file Carlos Simmerling (Tue Mar 31 2009 - 08:55:58 CDT)
  - Re: [AMBER] combine many coord files into trajectory file Peter Gannett (Tue Mar 31 2009 - 09:25:00 CDT)
[AMBER] Maxwell-Boltzmann distribution and ig=-1 Naser Alijabbari (Tue Mar 31 2009 - 20:35:43 CDT)
- Re: [AMBER] Maxwell-Boltzmann distribution and ig=-1 Carlos Simmerling (Tue Mar 31 2009 - 20:41:49 CDT)
  - Re: [AMBER] Maxwell-Boltzmann distribution and ig=-1 Naser Alijabbari (Tue Mar 31 2009 - 21:15:13 CDT)
[AMBER] a layer of water Nancy (Tue Mar 31 2009 - 20:37:51 CDT)
- Re: [AMBER] a layer of water oguz gurbulak (Wed Apr 01 2009 - 02:26:46 CDT)
[AMBER] constant-pH: appearance of not titrated residues during the Monte Carlo simulation Therese Malliavin (Wed Apr 01 2009 - 04:06:19 CDT)
- Re: [AMBER] constant-pH: appearance of not titrated residues during the Monte Carlo simulation David A. Case (Sat Apr 04 2009 - 08:20:28 CDT)
[AMBER] run protein with structural Ca+ sarah genare (Wed Apr 01 2009 - 06:01:24 CDT)
[AMBER] Failure to compile amber9 serial ifort gcc Francesco Pietra (Wed Apr 01 2009 - 06:04:18 CDT)
- Re: [AMBER] Failure to compile amber9 serial ifort gcc Alessandro Nascimento (Wed Apr 01 2009 - 06:09:42 CDT)
- Re: [AMBER] Failure to compile amber9 serial ifort gcc Francesco Pietra (Thu Apr 02 2009 - 06:16:36 CDT)
  - RE: [AMBER] Failure to compile amber9 serial ifort gcc Ross Walker (Thu Apr 02 2009 - 10:45:19 CDT)
    - Re: [AMBER] Failure to compile amber9 serial ifort gcc Francesco Pietra (Thu Apr 02 2009 - 11:00:46 CDT)
[AMBER] fillratio error in mmpbsa m m (Wed Apr 01 2009 - 06:42:45 CDT)
- Re: [AMBER] fillratio error in mmpbsa Han Ming (Wed Apr 01 2009 - 10:06:08 CDT)
- RE: [AMBER] fillratio error in mmpbsa Ray Luo (Wed Apr 01 2009 - 14:24:20 CDT)
[AMBER] calculation of Pi-Pi interaction energy aneesh cna (Wed Apr 01 2009 - 07:01:51 CDT)
[AMBER] calculation of Pi-Pi interaction energy Jacopo Sgrignani (Wed Apr 01 2009 - 07:24:28 CDT)
- Re: [AMBER] calculation of Pi-Pi interaction energy Jiri Sponer (Wed Apr 01 2009 - 07:38:49 CDT)
[AMBER] yacc parser Francesco Pietra (Wed Apr 01 2009 - 09:58:01 CDT)
- Re: [AMBER] yacc parser Mark Williamson (Wed Apr 01 2009 - 12:15:56 CDT)
- [AMBER] Fwd: yacc parser Francesco Pietra (Wed Apr 01 2009 - 15:53:01 CDT)
- Re: [AMBER] yacc parser David A. Case (Thu Apr 02 2009 - 07:03:06 CDT)
  - Re: [AMBER] yacc parser Francesco Pietra (Thu Apr 02 2009 - 10:37:53 CDT)
[AMBER] make test.serial.QMMM michael bane (Wed Apr 01 2009 - 10:44:51 CDT)
- Re: [AMBER] make test.serial.QMMM Seth Hayik (Wed Apr 01 2009 - 12:26:21 CDT)
[AMBER] ptraj and namd charmm dcd Sandro L. Fornili (Wed Apr 01 2009 - 10:59:37 CDT)
- Re: [AMBER] ptraj and namd charmm dcd Thomas Cheatham III (Wed Apr 01 2009 - 11:08:51 CDT)
[AMBER] AmberTools compilation error Kijeong Kwac (Wed Apr 01 2009 - 14:04:00 CDT)
- Re: [AMBER] AmberTools compilation error Marius Retegan (Wed Apr 01 2009 - 15:03:59 CDT)
[AMBER] Help: An error happened when I calculate mm/pbsa thirsty (Thu Apr 02 2009 - 03:12:25 CDT)
- Re: [AMBER] Help: An error happened when I calculate mm/pbsa Carlos Simmerling (Thu Apr 02 2009 - 06:19:04 CDT)
  - Re: [AMBER] Help: An error happened when I calculate mm/pbsa thirsty (Fri Apr 03 2009 - 02:11:19 CDT)
[AMBER] Umbrella test Arnaud (Thu Apr 02 2009 - 04:51:01 CDT)
- Re: [AMBER] Umbrella test David A. Case (Sat Apr 04 2009 - 08:12:13 CDT)
[AMBER] please help me out bharat lakhani (Thu Apr 02 2009 - 05:13:48 CDT)
- Re: [AMBER] please help me out David A. Case (Thu Apr 02 2009 - 12:48:10 CDT)
[AMBER] Counter-ions waleed zalloum (Thu Apr 02 2009 - 05:15:12 CDT)
[AMBER] problem in input balaji nagarajan (Thu Apr 02 2009 - 05:29:39 CDT)
- RE: [AMBER] problem in input Rausch, Felix (Thu Apr 02 2009 - 06:08:27 CDT)
  - RE: [AMBER] problem in input balaji nagarajan (Thu Apr 02 2009 - 15:23:18 CDT)
    - RE: [AMBER] problem in input Rausch, Felix (Fri Apr 03 2009 - 03:04:36 CDT)
[AMBER] number of waters in first and second solvation shell Siddharth Rastogi (Thu Apr 02 2009 - 06:40:21 CDT)
[AMBER] explicit ion with igb=1 Bala subramanian (Thu Apr 02 2009 - 08:39:10 CDT)
- Re: [AMBER] explicit ion with igb=1 Carlos Simmerling (Thu Apr 02 2009 - 08:53:54 CDT)
[AMBER] Averaging simulations Naser Alijabbari (Thu Apr 02 2009 - 10:21:41 CDT)
- Re: [AMBER] Averaging simulations Carlos Simmerling (Thu Apr 02 2009 - 10:24:28 CDT)
[AMBER] Error in trajin and rms Pansy Patel (Thu Apr 02 2009 - 13:58:47 CDT)
- Re: [AMBER] Error in trajin and rms Carlos Simmerling (Thu Apr 02 2009 - 14:19:39 CDT)
- RE: [AMBER] Error in trajin and rms iccy liu (Thu Apr 02 2009 - 14:19:16 CDT)
  - RE: [AMBER] Error in trajin and rms Pansy Patel (Thu Apr 02 2009 - 14:25:58 CDT)
[AMBER] parallel installation of amber on sun Per Jr. Greisen (Thu Apr 02 2009 - 14:02:47 CDT)
- Re: [AMBER] parallel installation of amber on sun Atro Tossavainen (Thu Apr 02 2009 - 15:23:05 CDT)
  - Re: [AMBER] parallel installation of amber on sun Per Jr. Greisen (Thu Apr 02 2009 - 15:38:54 CDT)
- Re: [AMBER] parallel installation of amber on sun Atro Tossavainen (Fri Apr 03 2009 - 04:39:25 CDT)
  - Re: [AMBER] parallel installation of amber on sun Per Jr. Greisen (Fri Apr 03 2009 - 05:22:45 CDT)
    - Re: [AMBER] parallel installation of amber on sun Atro Tossavainen (Fri Apr 03 2009 - 16:40:42 CDT)
    - Re: [AMBER] parallel installation of amber on sun Atro Tossavainen (Fri Apr 03 2009 - 17:33:52 CDT)
[AMBER] long polymer chain and image command in ptraj iccy liu (Thu Apr 02 2009 - 14:11:26 CDT)
- Re: [AMBER] long polymer chain and image command in ptraj Karl Kirschner (Mon Apr 06 2009 - 03:15:00 CDT)
[AMBER] Contour plot Beale, John (Thu Apr 02 2009 - 14:31:22 CDT)
- Re: [AMBER] Contour plot Gustavo Seabra (Thu Apr 02 2009 - 14:47:14 CDT)
[AMBER] How to delete the frames at specific intervals Mannan (Thu Apr 02 2009 - 20:16:49 CDT)
- Re: [AMBER] How to delete the frames at specific intervals Bala subramanian (Fri Apr 03 2009 - 04:55:35 CDT)
[AMBER] How to find out residence time of water molecules Mannan (Thu Apr 02 2009 - 20:52:36 CDT)
- Re: [AMBER] How to find out residence time of water molecules Bala subramanian (Fri Apr 03 2009 - 01:12:18 CDT)
- Re: [AMBER] How to find out residence time of water molecules Hannes Loeffler (Fri Apr 03 2009 - 02:31:32 CDT)
[AMBER] (no subject) chenquan (Fri Apr 03 2009 - 05:12:14 CDT)
- Re: [AMBER] (no subject) David A. Case (Fri Apr 03 2009 - 07:17:36 CDT)
[AMBER] How to create parameter file for unknown residue nicholus bhattacharjee (Fri Apr 03 2009 - 05:33:03 CDT)
- Re: [AMBER] How to create parameter file for unknown residue Marius Retegan (Fri Apr 03 2009 - 05:50:30 CDT)
[AMBER] Could not find angle parameter chenquan (Fri Apr 03 2009 - 05:46:47 CDT)
- Re: [AMBER] Could not find angle parameter Marius Retegan (Fri Apr 03 2009 - 05:58:47 CDT)
[AMBER] antechamber & multiple low-energy conformations Alessandro Nascimento (Fri Apr 03 2009 - 07:01:39 CDT)
[AMBER] amber9 serial compilation issues Francesco Pietra (Fri Apr 03 2009 - 13:38:12 CDT)
- Re: [AMBER] amber9 serial compilation issues David A. Case (Fri Apr 03 2009 - 15:01:02 CDT)
  - Re: [AMBER] amber9 serial compilation issues Francesco Pietra (Fri Apr 03 2009 - 17:04:17 CDT)
[AMBER] NALA-ALA-CALA peptide with antechamber Alan (Fri Apr 03 2009 - 11:33:17 CDT)
- Re: [AMBER] NALA-ALA-CALA peptide with antechamber David A. Case (Sat Apr 04 2009 - 08:04:32 CDT)
[AMBER] ptraj problem Ed Pate (Fri Apr 03 2009 - 15:13:37 CDT)
- Re: [AMBER] ptraj problem Thomas Cheatham III (Fri Apr 03 2009 - 15:23:21 CDT)
[AMBER] Generate AM1-CM2 charges using antechamber Sishi Tang (Fri Apr 03 2009 - 17:36:46 CDT)
[AMBER] parameter for amoeba Hemant Kumar (Sat Apr 04 2009 - 06:46:01 CDT)
[AMBER] LYN again Marius Retegan (Sat Apr 04 2009 - 08:12:09 CDT)
- Re: [AMBER] LYN again FyD (Sun Apr 05 2009 - 14:24:27 CDT)
  - Re: [AMBER] LYN again Marius Retegan (Mon Apr 06 2009 - 08:55:24 CDT)
    - Re: [AMBER] LYN again FyD (Mon Apr 06 2009 - 09:26:14 CDT)
[AMBER] deffision Nancy (Sat Apr 04 2009 - 09:30:50 CDT)
[AMBER] error in MM PBSA Vikas Sharma (Sat Apr 04 2009 - 12:06:57 CDT)
- Re: [AMBER] error in MM PBSA Hemant Gangwar (Sat Apr 04 2009 - 12:08:08 CDT)
- Re: [AMBER] error in MM PBSA David A. Case (Sat Apr 04 2009 - 16:16:42 CDT)
[AMBER] error in MM PBSA Vikas Sharma (Sun Apr 05 2009 - 01:09:35 CDT)
[AMBER] error in MM PBSA Vikas Sharma (Sun Apr 05 2009 - 23:27:21 CDT)
[AMBER] pmemd compilation/make failed - mkl_vml_service_threader_z_1i_c_1o Vijay Manickam Achari (Mon Apr 06 2009 - 02:27:24 CDT)
- Re: [AMBER] pmemd compilation/make failed -mkl_vml_service_threader_z_1i_c_1o Robert Duke (Mon Apr 06 2009 - 09:25:14 CDT)
  - Re: [AMBER] pmemd compilation/make failed -mkl_vml_service_threader_z_1i_c_1o Vijay Manickam Achari (Mon Apr 06 2009 - 23:25:36 CDT)
[AMBER] sander.MPI parallel run problem Dechang Li (Mon Apr 06 2009 - 02:44:12 CDT)
- Re: [AMBER] sander.MPI parallel run problem Carlos Simmerling (Mon Apr 06 2009 - 05:09:11 CDT)
  - Re: Re: [AMBER] sander.MPI parallel run problem Dechang Li (Mon Apr 06 2009 - 05:56:53 CDT)
    - Re: Re: [AMBER] sander.MPI parallel run problem Carlos Simmerling (Mon Apr 06 2009 - 06:02:13 CDT)
    - Re: Re: Re: [AMBER] sander.MPI parallel run problem Dechang Li (Mon Apr 06 2009 - 06:09:04 CDT)
[AMBER] faulty .rst file with "************" signs for the coordinates of a certain molecule. Soni Mufaddal Saifee (Mon Apr 06 2009 - 04:07:51 CDT)
- Re: [AMBER] faulty .rst file with "************" signs for the coordinates of a certain molecule. Carlos Simmerling (Mon Apr 06 2009 - 05:07:09 CDT)
  - Re: [AMBER] faulty .rst file with "************" signs for the coordinates of a certain molecule. Soni Mufaddal Saifee (Tue Apr 07 2009 - 23:19:25 CDT)
[AMBER] MM-PBSA error while running heat.in Vikas Sharma (Mon Apr 06 2009 - 04:32:55 CDT)
[AMBER] ssh and make test.parallel Francesco Pietra (Mon Apr 06 2009 - 04:58:39 CDT)
- Re: [AMBER] ssh and make test.parallel Atro Tossavainen (Mon Apr 06 2009 - 05:33:21 CDT)
  - Re: [AMBER] ssh and make test.parallel Francesco Pietra (Mon Apr 06 2009 - 09:29:19 CDT)
[AMBER] problem with secstruct action command in ptraj nicholus bhattacharjee (Mon Apr 06 2009 - 06:49:44 CDT)
[AMBER] testing RRR with antechamber Alan (Mon Apr 06 2009 - 07:10:27 CDT)
[AMBER] zwitterionic form of ARG and antechamber Alan (Mon Apr 06 2009 - 07:33:31 CDT)
[AMBER] Amber with AMOEBA force-field Tomasio, Susana (Mon Apr 06 2009 - 07:41:18 CDT)
- Re: [AMBER] Amber with AMOEBA force-field David A. Case (Mon Apr 06 2009 - 07:47:11 CDT)
  - RE: [AMBER] Amber with AMOEBA force-field Tomasio, Susana (Mon Apr 06 2009 - 07:49:28 CDT)
    - Re: [AMBER] Amber with AMOEBA force-field Wei Zhang (Mon Apr 06 2009 - 07:55:59 CDT)
- Re: [AMBER] Amber with AMOEBA force-field Wei Zhang (Mon Apr 06 2009 - 07:48:28 CDT)
  - RE: [AMBER] Amber with AMOEBA force-field Tomasio, Susana (Mon Apr 06 2009 - 07:52:01 CDT)
[AMBER] Sander waleed_zalloum_at_yahoo.com (Mon Apr 06 2009 - 08:17:34 CDT)
[AMBER] MM-PBSA: decompose energy error Lucilla Angeli (Mon Apr 06 2009 - 09:35:58 CDT)
- Re: [AMBER] MM-PBSA: decompose energy error Maria Mirza (Sun Aug 16 2009 - 14:49:06 CDT)
[AMBER] Sander Stalling Steve Seibold (Mon Apr 06 2009 - 11:21:51 CDT)
- Re: [AMBER] Sander Stalling Robert Duke (Mon Apr 06 2009 - 11:57:18 CDT)
- RE: [AMBER] Sander Stalling Ross Walker (Mon Apr 06 2009 - 11:58:58 CDT)
- [AMBER] sequence function taufik.alsarraj_at_utoronto.ca (Mon Apr 06 2009 - 12:03:20 CDT)
  - Re: [AMBER] sequence function taufik.alsarraj_at_utoronto.ca (Mon Apr 06 2009 - 12:06:50 CDT)
[AMBER] Do I need to modify the cap residues nicholus bhattacharjee (Mon Apr 06 2009 - 11:45:20 CDT)
- RE: [AMBER] Do I need to modify the cap residues Ross Walker (Mon Apr 06 2009 - 12:00:05 CDT)
  - Re: [AMBER] Do I need to modify the cap residues nicholus bhattacharjee (Mon Apr 06 2009 - 12:19:41 CDT)
[AMBER] Negative "number of measurements" in PTRAJ Jenny Iskrenova (Mon Apr 06 2009 - 12:28:59 CDT)
- Re: [AMBER] Negative "number of measurements" in PTRAJ Thomas Cheatham (Tue Apr 07 2009 - 11:57:28 CDT)
[AMBER] Amber on GPU Sasha Buzko (Mon Apr 06 2009 - 19:56:31 CDT)
- RE: [AMBER] Amber on GPU Ross Walker (Mon Apr 06 2009 - 20:14:07 CDT)
[AMBER] deffision coefficient Nancy (Mon Apr 06 2009 - 20:18:32 CDT)
- Re: [AMBER] deffision coefficient David A. Case (Mon Apr 06 2009 - 21:16:39 CDT)
[AMBER] A question about SMD force constant Jackie. J. Shen (Mon Apr 06 2009 - 20:40:13 CDT)
- Re: [AMBER] A question about SMD force constant Carlos Simmerling (Tue Apr 07 2009 - 05:32:09 CDT)
[AMBER] ambmask question Ed Pate (Mon Apr 06 2009 - 23:36:40 CDT)
[AMBER] Problems with running two separate jobs in the same time Antonija TomiÄ‡ (Tue Apr 07 2009 - 03:08:53 CDT)
- RE: [AMBER] Problems with running two separate jobs in the same time Ross Walker (Tue Apr 07 2009 - 10:01:14 CDT)
  - RE: [AMBER] Problems with running two separate jobs in the same time Antonija TomiÄ‡ (Thu Apr 09 2009 - 05:33:03 CDT)
[AMBER] how to add charge in metal ion bharat lakhani (Tue Apr 07 2009 - 04:11:23 CDT)
- RE: [AMBER] how to add charge in metal ion Ross Walker (Tue Apr 07 2009 - 10:01:14 CDT)
  - Re: [AMBER] how to add charge in metal ion bharat lakhani (Tue Apr 14 2009 - 07:49:44 CDT)
[AMBER] missing violations of the covalent geometry Helena P M Tossavainen (Tue Apr 07 2009 - 04:36:44 CDT)
- Re: [AMBER] missing violations of the covalent geometry David A. Case (Tue Apr 07 2009 - 06:10:42 CDT)
  - Re: [AMBER] missing violations of the covalent geometry Helena P M Tossavainen (Tue Apr 07 2009 - 07:10:16 CDT)
[AMBER] errors while testing Per Jr. Greisen (Tue Apr 07 2009 - 05:00:19 CDT)
- Re: [AMBER] errors while testing Atro Tossavainen (Tue Apr 07 2009 - 05:18:08 CDT)
  - Re: [AMBER] errors while testing Per Jr. Greisen (Wed Apr 08 2009 - 06:06:40 CDT)
[AMBER] Problem with CAP residues Tomasio, Susana (Tue Apr 07 2009 - 05:17:27 CDT)
- Re: [AMBER] Problem with CAP residues FyD (Tue Apr 07 2009 - 06:01:35 CDT)
[AMBER] TI production runs stop after a certain Step number Hannes Wallnoefer (Tue Apr 07 2009 - 06:48:45 CDT)
- Re: [AMBER] TI production runs stop after a certain Step number steinbrt_at_rci.rutgers.edu (Tue Apr 07 2009 - 09:49:57 CDT)
  - Re: [AMBER] TI production runs stop after a certain Step number Hannes Wallnoefer (Wed Apr 08 2009 - 06:48:31 CDT)
    - Re: [AMBER] TI production runs stop after a certain Step number steinbrt_at_rci.rutgers.edu (Wed Apr 08 2009 - 09:35:11 CDT)
    - Re: [AMBER] TI production runs stop after a certain Step number Hannes Wallnoefer (Wed Apr 08 2009 - 10:14:32 CDT)
- Re: [AMBER] TI production runs stop after a certain Step number Ilyas Yildirim (Tue Apr 07 2009 - 14:08:31 CDT)
[AMBER] problem in calculation of binding energy in final step (MM-PBSA) Maryam Hamzehee (Tue Apr 07 2009 - 08:59:03 CDT)
[AMBER] test/amoeba - forrtl: severe (64): input conversion error Tomasio, Susana (Tue Apr 07 2009 - 10:16:08 CDT)
- Re: [AMBER] test/amoeba - forrtl: severe (64): input conversion error David A. Case (Tue Apr 07 2009 - 11:29:18 CDT)
  - RE: [AMBER] test/amoeba - forrtl: severe (64): input conversion error Tomasio, Susana (Tue Apr 07 2009 - 11:34:57 CDT)
[AMBER] Testing parallel amber10: no libmkl_lapack.so Francesco Pietra (Tue Apr 07 2009 - 13:56:25 CDT)
- [AMBER] prmtop residue format taufik.alsarraj_at_utoronto.ca (Tue Apr 07 2009 - 15:04:25 CDT)
  - Re: [AMBER] prmtop residue format David A. Case (Tue Apr 07 2009 - 15:35:40 CDT)
    - Re: [AMBER] top2mol2 taufik.alsarraj_at_utoronto.ca (Tue Apr 07 2009 - 17:39:34 CDT)
    - [AMBER] ptraj randomizeions taufik.alsarraj_at_utoronto.ca (Tue Apr 07 2009 - 18:32:23 CDT)
- Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so Atro Tossavainen (Wed Apr 08 2009 - 04:35:17 CDT)
  - Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so Francesco Pietra (Wed Apr 08 2009 - 05:03:09 CDT)
[AMBER] PBSA Radii option quantum_mania_at_yahoo.com (Tue Apr 07 2009 - 14:31:18 CDT)
- [AMBER] Source of new CYX residue parameters in ff03ua Chris Moth (Tue Apr 07 2009 - 14:48:46 CDT)
  - [AMBER] Source of new CYX residue parameters in ff03ua Chris Moth (Tue Apr 14 2009 - 19:42:33 CDT)
    - RE: [AMBER] Source of new CYX residue parameters in ff03ua Ross Walker (Tue Apr 14 2009 - 23:08:14 CDT)
[AMBER] MMPB(GB)SA on trimer quantum_mania_at_yahoo.com (Tue Apr 07 2009 - 20:01:39 CDT)
[AMBER] compare MMPBSA result m m (Wed Apr 08 2009 - 01:28:06 CDT)
- RE: [AMBER] compare MMPBSA result Ray Luo (Wed Apr 08 2009 - 12:02:41 CDT)
[AMBER] problem with antechamber aneesh cna (Wed Apr 08 2009 - 01:32:32 CDT)
- Re:Re: [AMBER] problem with antechamber sculiujl (Fri Dec 04 2009 - 06:18:24 CST)
[AMBER] please help me out bharat lakhani (Wed Apr 08 2009 - 04:18:41 CDT)
- RE: [AMBER] please help me out Ross Walker (Wed Apr 08 2009 - 10:34:51 CDT)
  - Re: [AMBER] please help me out Hugh Heldenbrand (Wed Apr 08 2009 - 10:44:54 CDT)
    - Re: [AMBER] please help me out David A. Case (Wed Apr 08 2009 - 13:10:04 CDT)
  - [AMBER] ntwr taufik.alsarraj_at_utoronto.ca (Wed Apr 08 2009 - 16:45:01 CDT)
[AMBER] Failures of tests Per Jr. Greisen (Wed Apr 08 2009 - 10:41:34 CDT)
- RE: [AMBER] Failures of tests Seetin, Matthew (Wed Apr 08 2009 - 10:57:27 CDT)
  - Re: [AMBER] Failures of tests Per Jr. Greisen (Wed Apr 08 2009 - 11:17:16 CDT)
- Re: [AMBER] Failures of tests Atro Tossavainen (Wed Apr 08 2009 - 17:43:08 CDT)
  - Re: [AMBER] Failures of tests Per Jr. Greisen (Thu Apr 09 2009 - 07:52:32 CDT)
[AMBER] Thermodynamic Integration and belly Ignacio J. General (Wed Apr 08 2009 - 14:52:51 CDT)
[AMBER] force fields Mark M Huntress (Wed Apr 08 2009 - 19:23:38 CDT)
- RE: [AMBER] force fields Ross Walker (Wed Apr 08 2009 - 19:36:05 CDT)
- Re: [AMBER] force fields Gustavo Seabra (Wed Apr 15 2009 - 07:43:49 CDT)
[AMBER] please help me out bharat lakhani (Thu Apr 09 2009 - 00:10:22 CDT)
- Re: [AMBER] please help me out David A. Case (Thu Apr 09 2009 - 06:46:12 CDT)
[AMBER] how to plot this kind of map? lnin_1431_at_sina.com (Thu Apr 09 2009 - 03:36:45 CDT)
- Re: [AMBER] how to plot this kind of map? Dechang Li (Thu Apr 09 2009 - 03:46:16 CDT)
[AMBER] hpux sander.serial failure info Yiannis Georgiadis (Thu Apr 09 2009 - 17:28:28 CDT)
- Re: [AMBER] hpux sander.serial failure info David A. Case (Thu Apr 09 2009 - 06:56:51 CDT)
  - Re: [AMBER] hpux sander.serial failure info Yiannis Georgiadis (Wed Apr 15 2009 - 16:41:06 CDT)
    - Re: [AMBER] hpux sander.serial failure info David A. Case (Wed Apr 15 2009 - 07:07:45 CDT)
[AMBER] RST file waleed zalloum (Thu Apr 09 2009 - 09:06:37 CDT)
- Re: [AMBER] RST file David A. Case (Fri Apr 10 2009 - 07:21:19 CDT)
[AMBER] Release of R.E.D. Server FyD (Thu Apr 09 2009 - 03:31:30 CDT)
[AMBER] antechamber problems Jia Xu (Thu Apr 09 2009 - 12:12:44 CDT)
- Re: [AMBER] antechamber problems David A. Case (Thu Apr 09 2009 - 13:04:51 CDT)
- Re: [AMBER] antechamber problems Nicholas Musolino (Thu Apr 09 2009 - 13:03:45 CDT)
  - Re: [AMBER] antechamber problems Jia Xu (Fri Apr 10 2009 - 09:41:53 CDT)
[AMBER] Sander and multiple residues Dan Kaps (Thu Apr 09 2009 - 13:48:55 CDT)
- Re: [AMBER] Sander and multiple residues Carlos Simmerling (Thu Apr 09 2009 - 14:21:56 CDT)
  - Re: [AMBER] Sander and multiple residues Dan Kaps (Thu Apr 09 2009 - 15:02:46 CDT)
    - Re: [AMBER] Sander and multiple residues Carlos Simmerling (Thu Apr 09 2009 - 15:05:23 CDT)
    - Re: [AMBER] Sander and multiple residues Dan Kaps (Fri Apr 10 2009 - 07:56:53 CDT)
- Re: [AMBER] Sander and multiple residues Bill Ross (Thu Apr 09 2009 - 15:12:10 CDT)
  - Re: [AMBER] Sander and multiple residues Dan Kaps (Fri Apr 10 2009 - 07:57:54 CDT)
    - Re: [AMBER] Sander and multiple residues David A. Case (Fri Apr 10 2009 - 09:03:57 CDT)
    - Re: [AMBER] Sander and multiple residues Dan Kaps (Fri Apr 10 2009 - 10:01:08 CDT)
- Re: [AMBER] Sander and multiple residues Bill Ross (Fri Apr 10 2009 - 11:42:36 CDT)
  - Re: [AMBER] Sander and multiple residues Dan Kaps (Fri Apr 10 2009 - 12:46:49 CDT)
  - [AMBER] ptraj (vector and corrplane) taufik.alsarraj_at_utoronto.ca (Fri Apr 10 2009 - 19:45:46 CDT)
- Re: [AMBER] Sander and multiple residues Bill Ross (Fri Apr 10 2009 - 15:42:14 CDT)
[AMBER] igb=0 vs. igb=6 give different answers Hugh Heldenbrand (Thu Apr 09 2009 - 15:51:02 CDT)
- Re: [AMBER] igb=0 vs. igb=6 give different answers David A. Case (Thu Apr 09 2009 - 21:48:31 CDT)
[AMBER] basepair balaji nagarajan (Fri Apr 10 2009 - 00:30:57 CDT)
- Re: [AMBER] basepair Bala subramanian (Tue Apr 14 2009 - 06:09:21 CDT)
[AMBER] Amber 1.2 tools test suite failure? Jim Parker (Sat Apr 11 2009 - 12:41:54 CDT)
- RE: [AMBER] Amber 1.2 tools test suite failure? Ross Walker (Sat Apr 11 2009 - 13:00:45 CDT)
  - Re: [AMBER] Solved-Amber 1.2 tools test suite failure Jim Parker (Sat Apr 11 2009 - 14:29:55 CDT)
    - RE: [AMBER] Solved-Amber 1.2 tools test suite failure Ross Walker (Sat Apr 11 2009 - 14:51:13 CDT)
[AMBER] install and test Amber 10 parallel on Ubuntu 8.10 Jim Parker (Sat Apr 11 2009 - 19:20:25 CDT)
- [AMBER] Re: install and test Amber 10 parallel on Ubuntu 8.10 Jim Parker (Sat Apr 11 2009 - 23:47:19 CDT)
[AMBER] why amber10/dat/leap/gleap/ and amber10/dat/leap/parm Alan (Sun Apr 12 2009 - 04:30:15 CDT)
- Re: [AMBER] why amber10/dat/leap/gleap/ and amber10/dat/leap/parm Wei Zhang (Sun Apr 12 2009 - 08:24:47 CDT)
  - Re: [AMBER] why amber10/dat/leap/gleap/ and amber10/dat/leap/parm Alan (Sun Apr 12 2009 - 10:58:18 CDT)
[AMBER] problem with explicit solvent in TMD balaji nagarajan (Mon Apr 13 2009 - 06:37:21 CDT)
- Re: [AMBER] problem with explicit solvent in TMD Carlos Simmerling (Mon Apr 13 2009 - 06:41:41 CDT)
- RE: [AMBER] problem with explicit solvent in TMD Ross Walker (Mon Apr 13 2009 - 10:29:11 CDT)
[AMBER] Energy minimisation and NaN vivek.viv.sharma_at_gmail.com (Mon Apr 13 2009 - 06:55:55 CDT)
- Re: [AMBER] Energy minimisation and NaN David A. Case (Mon Apr 13 2009 - 14:28:10 CDT)
[AMBER] atom types in pdb files Dan Kaps (Mon Apr 13 2009 - 09:23:58 CDT)
- RE: [AMBER] atom types in pdb files Kristina Furse (Mon Apr 13 2009 - 11:30:05 CDT)
  - Re: [AMBER] atom types in pdb files Dan Kaps (Mon Apr 13 2009 - 14:29:43 CDT)
    - Re: [AMBER] atom types in pdb files David A. Case (Mon Apr 13 2009 - 15:25:04 CDT)
[AMBER] Thermodynamic Integration and belly Ignacio J. General (Mon Apr 13 2009 - 10:24:15 CDT)
- Re: [AMBER] Thermodynamic Integration and belly steinbrt_at_rci.rutgers.edu (Mon Apr 13 2009 - 11:46:19 CDT)
  - Re: [AMBER] Thermodynamic Integration and belly Ignacio J. General (Mon Apr 13 2009 - 12:26:16 CDT)
[AMBER] error saving prmtop and inpcrd files of complex in MM-PBSA Vikas Sharma (Mon Apr 13 2009 - 15:11:07 CDT)
[AMBER] restrained minimization quantum_mania_at_yahoo.com (Mon Apr 13 2009 - 19:12:35 CDT)
- Re: [AMBER] restrained minimization David A. Case (Mon Apr 13 2009 - 21:03:11 CDT)
[AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? Marek Malý (Mon Apr 13 2009 - 22:29:17 CDT)
- RE: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? Ross Walker (Mon Apr 13 2009 - 23:10:38 CDT)
  - Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? Marek Malý (Tue Apr 14 2009 - 18:18:18 CDT)
[AMBER] chosing complex in amber Vikas Sharma (Tue Apr 14 2009 - 00:18:43 CDT)
[AMBER] Questions on targeted MD with explicit solvent Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA]. (Tue Apr 14 2009 - 08:51:40 CDT)
[AMBER] [qm/mm] qmcharge for acidic a.a. in proteins sychen (Tue Apr 14 2009 - 11:33:03 CDT)
- RE: [AMBER] [qm/mm] qmcharge for acidic a.a. in proteins Ross Walker (Tue Apr 14 2009 - 14:45:06 CDT)
[AMBER] antechamber and wrong net charge with gasteiger method Alan (Tue Apr 14 2009 - 12:41:30 CDT)
- Re: [AMBER] antechamber and wrong net charge with gasteiger method David A. Case (Tue Apr 14 2009 - 13:42:14 CDT)
[AMBER] my FF m m (Tue Apr 14 2009 - 17:21:38 CDT)
- Re: [AMBER] my FF David A. Case (Wed Apr 15 2009 - 07:28:16 CDT)
[AMBER] water bonding with protein Mark M Huntress (Tue Apr 14 2009 - 21:55:39 CDT)
- Re: [AMBER] water bonding with protein David A. Case (Wed Apr 15 2009 - 06:58:17 CDT)
[AMBER] hbond_ptraj_eror balaji nagarajan (Wed Apr 15 2009 - 01:53:29 CDT)
[AMBER] mean of character in frcmod.ff03 chenquan (Wed Apr 15 2009 - 07:26:38 CDT)
- RE: [AMBER] mean of character in frcmod.ff03 Ross Walker (Wed Apr 15 2009 - 09:58:31 CDT)
  - RE: [AMBER] mean of character in frcmod.ff03 chenquan (Wed Apr 15 2009 - 18:36:32 CDT)
[AMBER] help- regarding - TMD balaji nagarajan (Wed Apr 15 2009 - 11:19:59 CDT)
- RE: [AMBER] help- regarding - TMD Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA]. (Wed Apr 15 2009 - 12:56:07 CDT)
  - RE: [AMBER] help- regarding - TMD balaji nagarajan (Thu Apr 16 2009 - 00:21:26 CDT)
    - RE: [AMBER] help- regarding - TMD Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA]. (Thu Apr 16 2009 - 08:30:22 CDT)
    - RE: [AMBER] help- regarding - TMD balaji nagarajan (Thu Apr 16 2009 - 12:01:39 CDT)
- RE: [AMBER] help- regarding - TMD Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA]. (Mon Apr 20 2009 - 10:05:38 CDT)
  - Re: [AMBER] help- regarding - TMD Carlos Simmerling (Mon Apr 20 2009 - 10:12:40 CDT)
[AMBER] please help me out bharat lakhani (Thu Apr 16 2009 - 01:41:08 CDT)
[AMBER] missing amber force field parameters Neha Gandhi (Thu Apr 16 2009 - 04:19:57 CDT)
- Re: [AMBER] missing amber force field parameters FyD (Thu Apr 16 2009 - 04:41:44 CDT)
[AMBER] pmemd in amber10 - compile failed in HPC Vijay Manickam Achari (Thu Apr 16 2009 - 05:13:49 CDT)
- Re: [AMBER] pmemd in amber10 - compile failed in HPC Robert Duke (Thu Apr 16 2009 - 07:24:45 CDT)
[AMBER] 1-4 vdW, GB MM difference Jimmy Heimdal (Thu Apr 16 2009 - 06:57:01 CDT)
- Re: [AMBER] 1-4 vdW, GB MM difference David A. Case (Thu Apr 16 2009 - 09:47:55 CDT)
[AMBER] ambertools failed - SMP IA64 Vijay Manickam Achari (Thu Apr 16 2009 - 08:17:34 CDT)
- Re: [AMBER] ambertools failed - SMP IA64 David A. Case (Thu Apr 16 2009 - 09:10:20 CDT)
[AMBER] Van der Waals atom types Antonio Morreale (Thu Apr 16 2009 - 09:39:14 CDT)
[AMBER] Amber and CHARMM summer school David A. Case (Thu Apr 16 2009 - 10:04:18 CDT)
[AMBER] Bad value during integer read by sander Collins Nganou (Thu Apr 16 2009 - 10:09:45 CDT)
[AMBER] sulfonamide parameters valeria.lapietra_at_unina.it (Thu Apr 16 2009 - 10:16:49 CDT)
[AMBER] polarizable force field for 18-crown-6 Gert von Helden (Thu Apr 16 2009 - 12:33:15 CDT)
- Re: [AMBER] polarizable force field for 18-crown-6 Piotr Cieplak (Fri Apr 17 2009 - 02:48:03 CDT)
[AMBER] help regarding force fields Vikas Sharma (Fri Apr 17 2009 - 01:06:32 CDT)
[AMBER] Right force fields Vikas Sharma (Fri Apr 17 2009 - 01:22:16 CDT)
- Re: [AMBER] Right force fields Patrick Schopf (Fri Apr 17 2009 - 07:48:14 CDT)
  - Re: [AMBER] Right force fields Vikas Sharma (Fri Apr 17 2009 - 08:14:04 CDT)
    - Re: [AMBER] Right force fields Patrick Schopf (Fri Apr 17 2009 - 08:34:04 CDT)
[AMBER] radius of gyration Beale, John (Fri Apr 17 2009 - 06:39:31 CDT)
[AMBER] Density in MD simulation Ibrahim Moustafa (Fri Apr 17 2009 - 11:09:16 CDT)
- Re: [AMBER] Density in MD simulation Carlos Simmerling (Fri Apr 17 2009 - 11:10:51 CDT)
  - Re: [AMBER] Density in MD simulation Ibrahim Moustafa (Fri Apr 17 2009 - 18:26:46 CDT)
[AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? quantum_mania_at_yahoo.com (Fri Apr 17 2009 - 12:52:28 CDT)
- Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? Lachele Foley (Lists) (Fri Apr 17 2009 - 13:13:49 CDT)
[AMBER] Backbone restraint Rilei Yu (Fri Apr 17 2009 - 21:30:38 CDT)
- Re: [AMBER] Backbone restraint Carlos Simmerling (Fri Apr 17 2009 - 21:35:26 CDT)
- Re: [AMBER] Backbone restraint Rilei Yu (Fri Apr 17 2009 - 22:29:12 CDT)
  - Re: [AMBER] Backbone restraint Carlos Simmerling (Sat Apr 18 2009 - 06:08:39 CDT)
    - Re: Re: [AMBER] Backbone restraint Rilei Yu (Mon Apr 20 2009 - 20:21:09 CDT)
  - Re: Re: [AMBER] Backbone restraint Jackie. J. Shen (Mon Apr 20 2009 - 20:12:13 CDT)
[AMBER] help_me to know the reason balaji nagarajan (Fri Apr 17 2009 - 23:30:07 CDT)
- Re: [AMBER] help_me to know the reason Carlos Simmerling (Sat Apr 18 2009 - 05:53:50 CDT)
[AMBER] please read this mail bharat lakhani (Sat Apr 18 2009 - 02:38:12 CDT)
- Re: [AMBER] please read this mail David A. Case (Sat Apr 18 2009 - 08:01:08 CDT)
[AMBER] about saltcon zgong.hust (Sat Apr 18 2009 - 21:45:53 CDT)
- Re: [AMBER] about saltcon Carlos Simmerling (Sun Apr 19 2009 - 05:49:57 CDT)
[AMBER] Atom type error Vikas Sharma (Sun Apr 19 2009 - 04:48:01 CDT)
- Re: [AMBER] Atom type error nicholus bhattacharjee (Sun Apr 19 2009 - 05:55:37 CDT)
  - Re: [AMBER] Atom type error Carlos Simmerling (Sun Apr 19 2009 - 06:06:07 CDT)
    - Re: [AMBER] Atom type error Vikas Sharma (Sun Apr 19 2009 - 11:49:53 CDT)
  - Re: [AMBER] Atom type error Vikas Sharma (Sun Apr 19 2009 - 11:50:28 CDT)
[AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail Marek Malý (Mon Apr 20 2009 - 06:52:36 CDT)
- Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail Karl Kirschner (Mon Apr 20 2009 - 07:27:45 CDT)
  - Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail Marek Malý (Mon Apr 20 2009 - 22:52:46 CDT)
- Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail FyD (Mon Apr 20 2009 - 09:50:12 CDT)
[AMBER] Partial interactions Ignacio J. General (Mon Apr 20 2009 - 16:07:24 CDT)
- Re: [AMBER] Partial interactions steinbrt_at_rci.rutgers.edu (Mon Apr 20 2009 - 16:47:35 CDT)
  - Re: [AMBER] Partial interactions Ignacio J. General (Tue Apr 21 2009 - 09:31:26 CDT)
[AMBER] My step size Vikas Sharma (Tue Apr 21 2009 - 01:50:16 CDT)
- RE: [AMBER] My step size Ross Walker (Tue Apr 21 2009 - 06:27:07 CDT)
  - Re: [AMBER] My step size Vikas Sharma (Tue Apr 21 2009 - 10:01:25 CDT)
  - Re: [AMBER] My step size Vikas Sharma (Tue Apr 21 2009 - 23:49:47 CDT)
[AMBER] atom numbers Vikas Sharma (Tue Apr 21 2009 - 06:12:27 CDT)
- Re: [AMBER] atom numbers David A. Case (Tue Apr 21 2009 - 06:54:37 CDT)
  - Re: [AMBER] atom numbers Vikas Sharma (Tue Apr 21 2009 - 10:33:12 CDT)
- Re: [AMBER] atom numbers Vikas Sharma (Tue Apr 21 2009 - 12:15:07 CDT)
- Re: [AMBER] atom numbers Vikas Sharma (Tue Apr 21 2009 - 13:36:35 CDT)
[AMBER] Number of LES copies in ptraj Thomas Exner (Tue Apr 21 2009 - 10:28:41 CDT)
[AMBER] Set start timestep for mdcrd traj output quantum_mania_at_yahoo.com (Tue Apr 21 2009 - 11:38:53 CDT)
- Re: [AMBER] Set start timestep for mdcrd traj output Carlos Simmerling (Tue Apr 21 2009 - 18:26:02 CDT)
  - Re: [AMBER] Set start timestep for mdcrd traj output Dong Xu (Tue Apr 21 2009 - 18:44:50 CDT)
[AMBER] Set start timestep for mdcrd traj output quantum_mania_at_yahoo.com (Tue Apr 21 2009 - 11:31:45 CDT)
[AMBER] Flexible ring simulation Dong Xu (Tue Apr 21 2009 - 18:04:55 CDT)
[AMBER] per atom energies in sander/pmemd Tamara Rogers (Tue Apr 21 2009 - 18:41:27 CDT)
[AMBER] Disulfide bond Dong Xu (Tue Apr 21 2009 - 20:37:46 CDT)
- Re: [AMBER] Disulfide bond Wei Zhang (Tue Apr 21 2009 - 20:46:19 CDT)
  - Re: [AMBER] Disulfide bond Dong Xu (Tue Apr 21 2009 - 21:41:02 CDT)
[AMBER] bintraj and amber 10 Naser Alijabbari (Wed Apr 22 2009 - 01:31:51 CDT)
- RE: [AMBER] bintraj and amber 10 Ross Walker (Wed Apr 22 2009 - 05:59:47 CDT)
  - Re: [AMBER] bintraj and amber 10 Naser Alijabbari (Wed Apr 22 2009 - 20:05:21 CDT)
[AMBER] help regarding step size Vikas Sharma (Wed Apr 22 2009 - 03:57:31 CDT)
- Re: [AMBER] help regarding step size Carlos Simmerling (Wed Apr 22 2009 - 05:13:54 CDT)
  - Re: [AMBER] help regarding step size Vikas Sharma (Wed Apr 22 2009 - 05:50:27 CDT)
    - Re: [AMBER] help regarding step size Carlos Simmerling (Wed Apr 22 2009 - 06:03:28 CDT)
    - Re: [AMBER] help regarding step size Vikas Sharma (Wed Apr 22 2009 - 23:40:33 CDT)
[AMBER] uncharged c and n terminal amino acids Christopher Materese (Wed Apr 22 2009 - 13:05:38 CDT)
- Re: [AMBER] uncharged c and n terminal amino acids David A. Case (Wed Apr 22 2009 - 13:16:19 CDT)
[AMBER] Problem with RNA hairpin unwinding in explicit water Sasha Buzko (Wed Apr 22 2009 - 16:55:58 CDT)
- RE: [AMBER] Problem with RNA hairpin unwinding in explicit water Seetin, Matthew (Wed Apr 22 2009 - 17:22:29 CDT)
- Re: [AMBER] Problem with RNA hairpin unwinding in explicit water Carlos Simmerling (Wed Apr 22 2009 - 17:25:47 CDT)
  - Re: [AMBER] Problem with RNA hairpin unwinding in explicit water Sasha Buzko (Wed Apr 22 2009 - 17:34:35 CDT)
- Re: [AMBER] Problem with RNA hairpin unwinding in explicit water Thomas Cheatham III (Wed Apr 22 2009 - 17:56:25 CDT)
  - Re: [AMBER] Problem with RNA hairpin unwinding in explicit water Sasha Buzko (Wed Apr 22 2009 - 18:10:55 CDT)
[AMBER] Amber Sulfate Ion Parameters Gary Clark (Wed Apr 22 2009 - 17:31:00 CDT)
- Re: [AMBER] Amber Sulfate Ion Parameters FyD (Thu Apr 23 2009 - 00:18:28 CDT)
- Re: [AMBER] Amber Sulfate Ion Parameters FyD (Thu Apr 23 2009 - 01:07:40 CDT)
  - Re: [AMBER] Amber Sulfate Ion Parameters Gary Clark (Thu Apr 23 2009 - 14:55:24 CDT)
[AMBER] error in output file Vikas Sharma (Thu Apr 23 2009 - 06:39:42 CDT)
- Re: [AMBER] error in output file Carlos Simmerling (Thu Apr 23 2009 - 06:42:02 CDT)
  - Re: [AMBER] error in output file Vikas Sharma (Thu Apr 23 2009 - 06:58:24 CDT)
[AMBER] nmod no run proprely in mmbsa mohamed mohamed (Thu Apr 23 2009 - 07:20:36 CDT)
- Re: [AMBER] nmod no run proprely in mmbsa David A. Case (Thu Apr 23 2009 - 07:47:44 CDT)
[AMBER] Regarding syntax for freezing different atoms Jorgen Simonsen (Thu Apr 23 2009 - 07:50:43 CDT)
- RE: [AMBER] Regarding syntax for freezing different atoms Ross Walker (Thu Apr 23 2009 - 08:24:55 CDT)
[AMBER] Amber Installation problem ÁÖÅÂ¼º (Thu Apr 23 2009 - 08:10:42 CDT)
- RE: [AMBER] Amber Installation problem Ross Walker (Thu Apr 23 2009 - 08:16:18 CDT)
[AMBER] NAB bug with parmbsc0 David A. Case (Thu Apr 23 2009 - 11:25:27 CDT)
Re: [AMBER] Problem with RNA hairpin unwinding in explicit water Bill Ross (Thu Apr 23 2009 - 12:53:40 CDT)
- Re: [AMBER] Problem with RNA hairpin unwinding in explicit water Sasha Buzko (Thu Apr 23 2009 - 12:55:58 CDT)
[AMBER] Unit name with loadMol2 command Nicholas Musolino (Thu Apr 23 2009 - 14:30:30 CDT)
- Re: [AMBER] Unit name with loadMol2 command David A. Case (Thu Apr 23 2009 - 17:54:02 CDT)
[AMBER] CY3 dye parameters jcmoore_at_student.umass.edu (Thu Apr 23 2009 - 16:42:59 CDT)
- Re: [AMBER] CY3 dye parameters FyD (Sat Apr 25 2009 - 01:04:22 CDT)
- Re: [AMBER] CY3 dye parameters Brent Krueger (Sat Apr 25 2009 - 14:33:40 CDT)
[AMBER] Amber Installation problem ÁÖÅÂ¼º (Thu Apr 23 2009 - 20:35:46 CDT)
[AMBER] Equilibrium bond lengths and angle values Dmitri Nilov (Fri Apr 24 2009 - 08:19:56 CDT)
- Re: [AMBER] Equilibrium bond lengths and angle values FyD (Fri Apr 24 2009 - 16:05:42 CDT)
  - Re: [AMBER] Equilibrium bond lengths and angle values Dmitri Nilov (Tue Apr 28 2009 - 05:56:38 CDT)
[AMBER] Simulated annealing waleed zalloum (Fri Apr 24 2009 - 09:31:36 CDT)
- Re: [AMBER] Simulated annealing Carlos Simmerling (Fri Apr 24 2009 - 09:49:40 CDT)
[AMBER] question Tatyana Fedotova (Fri Apr 24 2009 - 14:55:40 CDT)
[AMBER] restraint constant Dong Xu (Sat Apr 25 2009 - 17:15:22 CDT)
[AMBER] Papers on Amber package usage Andrew Voronkov (Sun Apr 26 2009 - 00:07:42 CDT)
- Re: [AMBER] Papers on Amber package usage David A. Case (Sun Apr 26 2009 - 07:48:31 CDT)
[AMBER] amber question Vikas Sharma (Sun Apr 26 2009 - 01:00:06 CDT)
- Re: [AMBER] amber question Barbault Florent (Sun Apr 26 2009 - 03:48:31 CDT)
  - Re: [AMBER] amber question Vikas Sharma (Sun Apr 26 2009 - 04:51:38 CDT)
  - Re: [AMBER] amber question Vikas Sharma (Sun Apr 26 2009 - 04:56:26 CDT)
[AMBER] Water-molecules sikander azam (Sun Apr 26 2009 - 08:11:33 CDT)
- Re: [AMBER] Water-molecules case (Sun Apr 26 2009 - 17:35:36 CDT)
  - [AMBER] MM-GBSA Free enegy decomposition Rajesh Raju (Mon Apr 27 2009 - 07:27:23 CDT)
[AMBER] Install ÁÖÅÂ¼º (Sun Apr 26 2009 - 08:45:45 CDT)
[AMBER] Using smd with fixed atom nandy_at_physics.iisc.ernet.in (Sun Apr 26 2009 - 09:57:45 CDT)
[AMBER] AmberTools compiling error Farly Walsh (Sun Apr 26 2009 - 19:40:38 CDT)
- RE: [AMBER] AmberTools compiling error Ross Walker (Sun Apr 26 2009 - 20:55:06 CDT)
  - Re: [AMBER] AmberTools compiling error Farly Walsh (Wed Apr 29 2009 - 14:49:27 CDT)
[AMBER] Error with calculation of the potential energy Per Jr. Greisen (Mon Apr 27 2009 - 06:03:44 CDT)
- Re: [AMBER] Error with calculation of the potential energy Carlos Simmerling (Mon Apr 27 2009 - 06:08:47 CDT)
  - Re: [AMBER] Error with calculation of the potential energy Per Jr. Greisen (Mon Apr 27 2009 - 12:11:32 CDT)
[AMBER] Mixing of forcefields in case of covaletly bonded systems Marek Malý (Mon Apr 27 2009 - 07:06:38 CDT)
[AMBER] Polarizable force field problem: non constant total Energy, EPOLZ is increasing Tommaso Cupido (Mon Apr 27 2009 - 09:10:12 CDT)
- Re: [AMBER] Polarizable force field problem: non constant total Energy, EPOLZ is increasing David A. Case (Mon Apr 27 2009 - 12:30:55 CDT)
  - Re: [AMBER] Polarizable force field problem: non constant total Energy, EPOLZ is increasing Piotr Cieplak (Mon Apr 27 2009 - 14:07:38 CDT)
  - [AMBER] ERROR In Restraint file. Catein Catherine (Tue Apr 28 2009 - 10:12:34 CDT)
[AMBER] pmemd compilation error john smith (Mon Apr 27 2009 - 22:30:21 CDT)
- Re: [AMBER] pmemd compilation error Robert Duke (Mon Apr 27 2009 - 23:09:15 CDT)
  - Re: [AMBER] pmemd compilation error john smith (Tue May 05 2009 - 06:20:08 CDT)
[AMBER] Best rms fit for correlation and covariance analysis Cihan Aydin (Tue Apr 28 2009 - 00:02:14 CDT)
[AMBER] dipole autocorrelation functions aneesh cna (Tue Apr 28 2009 - 01:23:05 CDT)
Fwd: [AMBER] MM-GBSA Free enegy decomposition Rajesh Raju (Tue Apr 28 2009 - 06:28:17 CDT)
[AMBER] transport properties oguz gurbulak (Tue Apr 28 2009 - 09:11:05 CDT)
[AMBER] reg-TMD balaji nagarajan (Tue Apr 28 2009 - 10:23:34 CDT)
- Re: [AMBER] reg-TMD Carlos Simmerling (Tue Apr 28 2009 - 12:48:18 CDT)
  - RE: [AMBER] reg-TMD balaji nagarajan (Tue Apr 28 2009 - 23:16:17 CDT)
Re: [AMBER] Best rms fit for correlation and covariance analysis Bill Ross (Tue Apr 28 2009 - 11:57:10 CDT)
[AMBER] Restraining counterions? Francesco Pietra (Tue Apr 28 2009 - 12:32:18 CDT)
Re: [AMBER] Restraining counterions? Bill Ross (Tue Apr 28 2009 - 13:59:52 CDT)
[AMBER] ANAL problems E.M. (Tue Apr 28 2009 - 15:12:04 CDT)
Re: [AMBER] ANAL problems Bill Ross (Tue Apr 28 2009 - 15:40:59 CDT)
- Re: [AMBER] ANAL problems Edward M (Tue Apr 28 2009 - 18:01:34 CDT)
[AMBER] Using AMBER force fields in NAMD Michael Zimmermann (Tue Apr 28 2009 - 16:25:56 CDT)
- RE: [AMBER] Using AMBER force fields in NAMD Ross Walker (Tue Apr 28 2009 - 17:17:06 CDT)
  - RE: [AMBER] Using AMBER force fields in NAMD Piotr Cieplak (Tue Apr 28 2009 - 17:23:15 CDT)
  - RE: [AMBER] Using AMBER force fields in NAMD Thomas Cheatham III (Tue Apr 28 2009 - 17:45:15 CDT)
[AMBER] parallel problem of QM/MM calculation for AMBER 9 liu junjun (Tue Apr 28 2009 - 16:53:06 CDT)
- RE: [AMBER] parallel problem of QM/MM calculation for AMBER 9 Ross Walker (Tue Apr 28 2009 - 17:24:12 CDT)
  - Re: [AMBER] parallel problem of QM/MM calculation for AMBER 9 liu junjun (Tue Apr 28 2009 - 21:18:31 CDT)
[AMBER] The PDB file was not recognized by Amber, what can i do? Houyang Chen (Tue Apr 28 2009 - 17:00:05 CDT)
- Re: [AMBER] The PDB file was not recognized by Amber, what can i do? Carlos Simmerling (Tue Apr 28 2009 - 17:03:57 CDT)
- Re: [AMBER] The PDB file was not recognized by Amber, what can i do? Barbault Florent (Tue Apr 28 2009 - 18:00:55 CDT)
  - RE: [AMBER] The PDB file was not recognized by Amber, what can i do? Houyang Chen (Tue Apr 28 2009 - 22:42:39 CDT)
    - RE: [AMBER] The PDB file was not recognized by Amber, what can i do? Ross Walker (Tue Apr 28 2009 - 22:56:27 CDT)
    - Re: [AMBER] The PDB file was not recognized by Amber, what can i do? Barbault Florent (Wed Apr 29 2009 - 01:56:09 CDT)
- Re: [AMBER] The PDB file was not recognized by Amber, what can i do? Markus Kaukonen (Wed Apr 29 2009 - 02:16:30 CDT)
  - RE: [AMBER] The PDB file was not recognized by Amber, what can i do? Houyang Chen (Wed Apr 29 2009 - 17:17:51 CDT)
[AMBER] Nonterminal, was not found in name map Sunita Patel (Tue Apr 28 2009 - 19:50:08 CDT)
- RE: [AMBER] Nonterminal, was not found in name map Ross Walker (Tue Apr 28 2009 - 21:49:50 CDT)
- RE: [AMBER] Nonterminal, was not found in name map Bill Ross (Wed Apr 29 2009 - 00:05:12 CDT)
[AMBER] REd program! R. A. (Tue Apr 28 2009 - 23:37:38 CDT)
- Re: [AMBER] REd program! FyD (Wed Apr 29 2009 - 08:53:12 CDT)
[AMBER] (no subject) waleed zalloum (Wed Apr 29 2009 - 07:15:12 CDT)
- Re: [AMBER] (no subject) David A. Case (Wed Apr 29 2009 - 12:56:28 CDT)
[AMBER] input error in TI calculation Hannes Wallnoefer (Wed Apr 29 2009 - 10:40:58 CDT)
- Re: [AMBER] input error in TI calculation David A. Case (Wed Apr 29 2009 - 13:48:04 CDT)
[AMBER] chain restrain x TI Josmar R. da Rocha (Wed Apr 29 2009 - 17:04:52 CDT)
- Re: [AMBER] chain restrain x TI David A. Case (Thu Apr 30 2009 - 13:01:13 CDT)
  - Re: [AMBER] chain restrain x TI Josmar R. da Rocha (Sat May 02 2009 - 12:09:53 CDT)
[AMBER] Amber FF and Glycam Dong Xu (Wed Apr 29 2009 - 20:42:55 CDT)
- Re: [AMBER] Amber FF and Glycam Lachele Foley (Lists) (Thu Apr 30 2009 - 12:16:17 CDT)
- Re: [AMBER] Amber FF and Glycam Carlos Simmerling (Thu Apr 30 2009 - 13:36:21 CDT)
  - Re: [AMBER] Amber FF and Glycam Hannes Loeffler (Fri May 01 2009 - 03:33:34 CDT)
[AMBER] MM-PBSA energy decomposition Dong Xu (Wed Apr 29 2009 - 21:03:34 CDT)
- Re: [AMBER] MM-PBSA energy decomposition Hannes Kopitz (Thu Apr 30 2009 - 05:37:35 CDT)
[AMBER] hbond-error in amber9 balaji nagarajan (Wed Apr 29 2009 - 21:09:17 CDT)
- Re: [AMBER] hbond-error in amber9 Alessandro S. Nascimento (Thu Apr 30 2009 - 05:46:02 CDT)
[AMBER] Influence about HIS-HIE-HIS-HIP Rilei Yu (Wed Apr 29 2009 - 22:25:48 CDT)
- Re: [AMBER] Influence about HIS-HIE-HIS-HIP David A. Case (Thu Apr 30 2009 - 09:27:02 CDT)
- Re: [AMBER] Influence about HIS-HIE-HIS-HIP Rilei Yu (Thu Apr 30 2009 - 19:37:17 CDT)
[AMBER] how to add charge on metal ions bharat lakhani (Thu Apr 30 2009 - 01:44:46 CDT)
[AMBER] Request an error Collins Nganou (Thu Apr 30 2009 - 12:41:48 CDT)
[AMBER] (no subject) Collins Nganou (Thu Apr 30 2009 - 14:34:36 CDT)
- Re: [AMBER] (no subject) David A. Case (Thu Apr 30 2009 - 15:16:35 CDT)
[AMBER] Make parallel test faillure Collins Nganou (Thu Apr 30 2009 - 14:36:55 CDT)
- RE: [AMBER] Make parallel test faillure Ross Walker (Thu Apr 30 2009 - 14:48:06 CDT)
RE: [Subject Filtered] [AMBER] hbond-error in amber9 8% Hopkins, Robert (Thu Apr 30 2009 - 19:02:34 CDT)
- RE: [Subject Filtered] [AMBER] hbond-error in amber9 8% Thomas Cheatham III (Fri May 01 2009 - 13:07:40 CDT)
[AMBER] unable to start xleap Jayalakshmi Sridhar (Fri May 01 2009 - 13:32:27 CDT)
- Re: [AMBER] unable to start xleap Wei Zhang (Fri May 01 2009 - 13:39:03 CDT)
[AMBER] charge of Fe-heme ¶ê» (Fri May 01 2009 - 14:08:12 CDT)
- Re: [AMBER] charge of Fe-heme David A. Case (Fri May 01 2009 - 17:52:45 CDT)
- Re: [AMBER] charge of Fe-heme FyD (Sat May 02 2009 - 11:02:48 CDT)
[AMBER] how to assign radii parameters to certain atoms when fitting RESP charge using antechamber Ye MEI (Sat May 02 2009 - 07:00:06 CDT)
[AMBER] how to assign radii parameters to certain atoms when fitting RESP charge using antechamber Ye MEI (Sat May 02 2009 - 07:01:20 CDT)
- Re: [AMBER] how to assign radii parameters to certain atoms when fitting RESP charge using antechamber FyD (Sat May 02 2009 - 11:06:28 CDT)
[AMBER] equilibration stops for dimer simulation with REMD Sunita Patel (Sat May 02 2009 - 15:11:48 CDT)
- Re: [AMBER] equilibration stops for dimer simulation with REMD Carlos Simmerling (Sun May 03 2009 - 06:11:07 CDT)
- Re: [AMBER] equilibration stops for dimer simulation with REMD Sunita Patel (Sun May 03 2009 - 20:30:05 CDT)
- Re: [AMBER] equilibration stops for dimer simulation with REMD Sunita Patel (Tue May 05 2009 - 11:33:40 CDT)
  - Re: [AMBER] equilibration stops for dimer simulation with REMD Carlos Simmerling (Tue May 05 2009 - 11:39:52 CDT)
- Re: [AMBER] equilibration stops for dimer simulation with REMD Sunita Patel (Tue May 05 2009 - 12:26:09 CDT)
  - Re: [AMBER] equilibration stops for dimer simulation with REMD Carlos Simmerling (Tue May 05 2009 - 12:32:42 CDT)
- Re: [AMBER] equilibration stops for dimer simulation with REMD Sunita Patel (Thu May 07 2009 - 13:35:59 CDT)
[AMBER] QM/MM assigns Cd to C, Se to S C Liu (Sat May 02 2009 - 21:09:27 CDT)
- RE: [AMBER] QM/MM assigns Cd to C, Se to S Ross Walker (Sat May 02 2009 - 23:45:41 CDT)
- RE: [AMBER] QM/MM assigns Cd to C, Se to S Ross Walker (Fri May 08 2009 - 02:16:09 CDT)
[AMBER] LCPO or Molsurf? Dong Xu (Sat May 02 2009 - 22:14:55 CDT)
[AMBER] High energy during minimization aneesh cna (Sat May 02 2009 - 23:26:16 CDT)
- Re: [AMBER] High energy during minimization David A. Case (Sun May 03 2009 - 08:40:22 CDT)
- Re: [AMBER] High energy during minimization Bill Ross (Sun May 03 2009 - 13:00:32 CDT)
  - Re: [AMBER] High energy during minimization aneesh cna (Wed May 06 2009 - 00:58:00 CDT)
    - RE: [AMBER] High energy during minimization Ross Walker (Wed May 06 2009 - 01:24:30 CDT)
[AMBER] help with RESP tutorial using antechamber and gaussian Josmar R. da Rocha (Sun May 03 2009 - 12:59:23 CDT)
[AMBER] make test.parallel.MM error Collins Nganou (Sun May 03 2009 - 16:20:51 CDT)
[AMBER] prmtop Mark M Huntress (Sun May 03 2009 - 18:20:39 CDT)
- RE: [AMBER] prmtop Ross Walker (Sun May 03 2009 - 21:18:04 CDT)
[AMBER] problem with cutoff Yunjie Zhao (Sun May 03 2009 - 22:53:00 CDT)
- RE: [AMBER] problem with cutoff Ross Walker (Mon May 04 2009 - 00:02:04 CDT)
  - Re: [AMBER] problem with cutoff Yunjie Zhao (Mon May 04 2009 - 07:58:00 CDT)
    - RE: [AMBER] problem with cutoff Ross Walker (Mon May 04 2009 - 10:35:40 CDT)
[AMBER] "Parameter file not generated" Remya S R (Mon May 04 2009 - 01:17:23 CDT)
[AMBER] Parameter file not saved Remya S R (Mon May 04 2009 - 01:30:19 CDT)
[AMBER] creating new residue adds none wanted ter Jorgen Simonsen (Mon May 04 2009 - 02:49:47 CDT)
- [AMBER] Error message for tutorial 1 (run in parallel) Catein Catherine (Mon May 04 2009 - 04:05:17 CDT)
  - Re: [AMBER] Error message for tutorial 1 (run in parallel) David A. Case (Mon May 04 2009 - 07:40:36 CDT)
    - RE: [AMBER] Error message for tutorial 1 (run in parallel) Catein Catherine (Mon May 04 2009 - 08:31:05 CDT)
- Re: [AMBER] creating new residue adds none wanted ter David A. Case (Mon May 04 2009 - 08:35:41 CDT)
  - Re: [AMBER] creating new residue adds none wanted ter Jorgen Simonsen (Mon May 04 2009 - 09:09:08 CDT)
[AMBER] MM_PBSA problem in Amber 9 Sean Zhao (Mon May 04 2009 - 04:09:14 CDT)
[AMBER] Script for parallel runs Catein Catherine (Mon May 04 2009 - 04:17:42 CDT)
- [AMBER] Script for parallel runs 2 Catein Catherine (Mon May 04 2009 - 04:41:58 CDT)
  - RE: [AMBER] Script for parallel runs 2 Ross Walker (Mon May 04 2009 - 10:39:27 CDT)
- Re: [AMBER] Script for parallel runs Gustavo Seabra (Tue May 05 2009 - 11:31:38 CDT)
[AMBER] Non-zero internal energy in single trajectory MM-PBSA calculations Dmitry Osolodkin (Mon May 04 2009 - 04:24:59 CDT)
[AMBER] normal mode analysis Hannes Wallnoefer (Mon May 04 2009 - 04:39:16 CDT)
- Re: [AMBER] normal mode analysis David A. Case (Mon May 04 2009 - 08:37:02 CDT)
  - [AMBER] Why the job idle before the sentence "| Running AMBER/MPI version on 2 nodes"? Catein Catherine (Mon May 04 2009 - 10:16:08 CDT)
  - Re: [AMBER] normal mode analysis Hannes Wallnoefer (Mon May 04 2009 - 10:56:11 CDT)
[AMBER] Parameter file not saved Remya S R (Mon May 04 2009 - 07:03:08 CDT)
- Re: [AMBER] Parameter file not saved Carlos Simmerling (Mon May 04 2009 - 07:19:14 CDT)
[AMBER] MMPBSA- interaction energy for every frame Jack Colis (Mon May 04 2009 - 09:38:38 CDT)
- RE: [AMBER] MMPBSA- interaction energy for every frame Wei Huang (Mon May 04 2009 - 09:58:26 CDT)
  - Re: [AMBER] MMPBSA- interaction energy for every frame Jack Colis (Tue May 05 2009 - 03:22:35 CDT)
[AMBER] QM/MM Syed Tarique Moin (Mon May 04 2009 - 10:32:29 CDT)
- RE: [AMBER] QM/MM Ross Walker (Mon May 04 2009 - 12:47:21 CDT)
[AMBER] xleap segmentation fault Jayalakshmi Sridhar (Mon May 04 2009 - 10:50:06 CDT)
[AMBER] Error in PMEMD run Marek Malý (Mon May 04 2009 - 20:23:33 CDT)
- Re: [AMBER] Error in PMEMD run Robert Duke (Mon May 04 2009 - 20:35:54 CDT)
  - Re: [AMBER] Error in PMEMD run Marek Malý (Mon May 04 2009 - 21:19:20 CDT)
Re: [AMBER] Error in PMEMD run Robert Duke (Fri May 08 2009 - 13:14:12 CDT)
- Re: [AMBER] Error in PMEMD run Marek Malý (Fri May 08 2009 - 13:27:20 CDT)
Re: [AMBER] Error in PMEMD run Marek Malý (Fri May 08 2009 - 11:38:27 CDT)
- Re: [AMBER] Error in PMEMD run Gustavo Seabra (Fri May 08 2009 - 12:28:35 CDT)
  - Re: [AMBER] Error in PMEMD run Marek Malý (Fri May 08 2009 - 12:57:36 CDT)
[AMBER] A confusion about tutorial B1 Houyang Chen (Tue May 05 2009 - 00:01:31 CDT)
- RE: [AMBER] A confusion about tutorial B1 Ross Walker (Tue May 05 2009 - 00:18:43 CDT)
  - RE: [AMBER] A confusion about tutorial B1 Houyang Chen (Tue May 05 2009 - 00:24:39 CDT)
- Re: [AMBER] A confusion about tutorial B1 Carlos Simmerling (Tue May 05 2009 - 05:11:43 CDT)
[AMBER] Problem in production run nicholus bhattacharjee (Tue May 05 2009 - 00:50:07 CDT)
- Re: [AMBER] Problem in production run Carlos Simmerling (Tue May 05 2009 - 05:07:11 CDT)
[AMBER] Suggestion for restraining chain of a protein nicholus bhattacharjee (Tue May 05 2009 - 01:29:54 CDT)
- Re: [AMBER] Suggestion for restraining chain of a protein Carlos Simmerling (Tue May 05 2009 - 05:05:16 CDT)
  - Re: [AMBER] Suggestion for restraining chain of a protein nicholus bhattacharjee (Tue May 05 2009 - 07:20:44 CDT)
    - Re: [AMBER] Suggestion for restraining chain of a protein Carlos Simmerling (Tue May 05 2009 - 07:27:05 CDT)
[AMBER] Charge problem Remya S R (Tue May 05 2009 - 06:43:47 CDT)
- Re: [AMBER] Charge problem Carlos Simmerling (Tue May 05 2009 - 07:16:32 CDT)
  - Re: [AMBER] Charge problem Remya S R (Tue May 05 2009 - 07:19:51 CDT)
    - Re: [AMBER] Charge problem Carlos Simmerling (Tue May 05 2009 - 07:58:31 CDT)
[AMBER] Problems with PMEMD installation for AMBER10 German Erlenkamp (Tue May 05 2009 - 07:40:56 CDT)
- Re: [AMBER] Problems with PMEMD installation for AMBER10 Robert Duke (Tue May 05 2009 - 08:00:54 CDT)
  - Re: [AMBER] Problems with PMEMD installation for AMBER10 German Erlenkamp (Tue May 05 2009 - 08:07:13 CDT)
    - Re: [AMBER] Problems with PMEMD installation for AMBER10 Robert Duke (Tue May 05 2009 - 08:48:06 CDT)
    - Re: [AMBER] Problems with PMEMD installation for AMBER10 German Erlenkamp (Thu May 07 2009 - 02:18:36 CDT)
[AMBER] skip parallel test Collins Nganou (Tue May 05 2009 - 08:09:00 CDT)
- Re: [AMBER] skip parallel test David A. Case (Tue May 05 2009 - 10:34:14 CDT)
- RE: [AMBER] skip parallel test Ross Walker (Tue May 05 2009 - 10:43:34 CDT)
[AMBER] Can bond clevage & formation conducted by qm/mm via sander? sychen (Tue May 05 2009 - 08:12:32 CDT)
- Re: [AMBER] Can bond clevage & formation conducted by qm/mm via sander? Gustavo Seabra (Tue May 05 2009 - 12:04:37 CDT)
- Re: [AMBER] Can bond clevage & formation conducted by qm/mm via sander? Mahmoud A. A. Ibrahim (Tue May 05 2009 - 12:15:18 CDT)
  - Re: [AMBER] Can bond clevage & formation conducted by qm/mm via sander? Gustavo Seabra (Tue May 05 2009 - 12:28:10 CDT)
[AMBER] Error: cannot run prepgen Rose Tamil (Tue May 05 2009 - 10:20:52 CDT)
[AMBER] difference in temperature Naser Alijabbari (Tue May 05 2009 - 19:02:28 CDT)
- Re: [AMBER] difference in temperature David A. Case (Wed May 06 2009 - 07:08:01 CDT)
  - Re: [AMBER] difference in temperature Naser Alijabbari (Wed May 06 2009 - 07:29:48 CDT)
[AMBER] ntf, ntc with softcore potentials and TI in amber10 Matthew Wilce (Tue May 05 2009 - 20:33:28 CDT)
- Re: [AMBER] ntf, ntc with softcore potentials and TI in amber10 steinbrt_at_rci.rutgers.edu (Tue May 05 2009 - 22:39:02 CDT)
[AMBER] Error in MM PBSA Vikas Sharma (Wed May 06 2009 - 03:35:57 CDT)
[AMBER] Conformation of sulfated Glucosamine Neha Gandhi (Wed May 06 2009 - 04:54:31 CDT)
- RE: [AMBER] Conformation of sulfated Glucosamine Matthew Tessier (Wed May 06 2009 - 10:19:22 CDT)
[AMBER] positive value of binding enrgy after MM PBSA Vikas Sharma (Wed May 06 2009 - 10:07:03 CDT)
[AMBER] xleap input pdb problem Majeed Shaik (Wed May 06 2009 - 13:47:45 CDT)
- Re: [AMBER] xleap input pdb problem David A. Case (Wed May 06 2009 - 21:16:10 CDT)
  - [AMBER] Error in parallel run Catein Catherine (Wed May 06 2009 - 21:46:02 CDT)
  - [AMBER] AMBER for dual core processor? Catein Catherine (Thu May 07 2009 - 03:05:17 CDT)
    - RE: [AMBER] AMBER for dual core processor? Ross Walker (Thu May 07 2009 - 10:26:09 CDT)
[AMBER] multiple chain specification in Sander Siddharth Rastogi (Wed May 06 2009 - 22:17:57 CDT)
- Re: [AMBER] multiple chain specification in Sander Carlos Simmerling (Thu May 07 2009 - 05:19:09 CDT)
  - Re: [AMBER] multiple chain specification in Sander Siddharth Rastogi (Thu May 07 2009 - 15:29:28 CDT)
[AMBER] ptraj PCA - Highest Eigenvalues or First 2 Calculated? Patrick Gedeon (Wed May 06 2009 - 23:12:39 CDT)
- Re: [AMBER] ptraj PCA - Highest Eigenvalues or First 2 Calculated? Hannes Loeffler (Thu May 07 2009 - 02:47:23 CDT)
[AMBER] Error in binding energy (MM PBSA) Vikas Sharma (Thu May 07 2009 - 00:47:33 CDT)
- Re: [AMBER] Error in binding energy (MM PBSA) David A. Case (Thu May 07 2009 - 06:33:20 CDT)
  - Re: [AMBER] Error in binding energy (MM PBSA) Vikas Sharma (Thu May 07 2009 - 08:29:22 CDT)
- RE: [AMBER] Error in binding energy (MM PBSA) Ray Luo (Thu May 07 2009 - 13:12:18 CDT)
  - Re: [AMBER] Error in binding energy (MM PBSA) Vikas Sharma (Fri May 08 2009 - 01:42:32 CDT)
    - RE: [AMBER] Error in binding energy (MM PBSA) Ray Luo (Fri May 08 2009 - 11:42:58 CDT)
  - Re: [AMBER] Error in binding energy (MM PBSA) Vikas Sharma (Fri May 08 2009 - 01:50:40 CDT)
[AMBER] free enrgy error in MM PBSA Vikas Sharma (Thu May 07 2009 - 05:11:44 CDT)
[AMBER] dftb_disper problem Fernando Martín García (Thu May 07 2009 - 07:30:25 CDT)
- Re: [AMBER] dftb_disper problem Gustavo Seabra (Thu May 07 2009 - 08:01:42 CDT)
  - Re: [Barracuda SPAM] Re: [AMBER] dftb_disper problem Fernando Martín García (Thu May 07 2009 - 08:32:06 CDT)
  - Re: [AMBER] dftb_disper problem Fernando Martín García (Fri May 08 2009 - 07:43:19 CDT)
[AMBER] ambertools for NAMD Jorgen Simonsen (Thu May 07 2009 - 07:35:24 CDT)
- Re: [AMBER] ambertools for NAMD Carlos Simmerling (Thu May 07 2009 - 08:36:27 CDT)
  - Re: [AMBER] ambertools for NAMD David A. Case (Thu May 07 2009 - 09:09:55 CDT)
[AMBER] Problems in the result of MM_PBSA Sean Zhao (Thu May 07 2009 - 20:30:24 CDT)
- RE: [AMBER] Problems in the result of MM_PBSA Ray Luo (Thu May 07 2009 - 21:02:58 CDT)
- Re: [AMBER] Problems in the result of MM_PBSA David A. Case (Fri May 08 2009 - 07:45:19 CDT)
  - Re: [AMBER] Problems in the result of MM_PBSA Sean Zhao (Fri May 08 2009 - 22:44:29 CDT)
[AMBER] RE: Listing gaff parameters in frcmod Bokun Cho (Thu May 07 2009 - 23:20:46 CDT)
- RE: [AMBER] RE: Listing gaff parameters in frcmod Ross Walker (Thu May 07 2009 - 23:34:08 CDT)
  - Re: [AMBER] RE: Listing gaff parameters in frcmod Bokun Cho (Fri May 08 2009 - 00:00:47 CDT)
    - Re: [AMBER] RE: Listing gaff parameters in frcmod steinbrt_at_rci.rutgers.edu (Fri May 08 2009 - 09:23:45 CDT)
[AMBER] Error in binding energy (MM PBSA) Vikas Sharma (Fri May 08 2009 - 01:44:33 CDT)
- Re: [AMBER] Error in binding energy (MM PBSA) Vikas Sharma (Sat May 09 2009 - 02:19:20 CDT)
  - RE: [AMBER] Error in binding energy (MM PBSA) Ray Luo (Sat May 09 2009 - 20:39:05 CDT)
    - Re: [AMBER] Error in binding energy (MM PBSA) Vikas Sharma (Sun May 10 2009 - 04:03:07 CDT)
- Re: [AMBER] Error in binding energy (MM PBSA) Vikas Sharma (Sat May 09 2009 - 02:20:09 CDT)
- Re: [AMBER] Error in binding energy (MM PBSA) Vikas Sharma (Mon May 11 2009 - 03:08:28 CDT)
  - RE: [AMBER] Error in binding energy (MM PBSA) Ray Luo (Mon May 11 2009 - 13:14:20 CDT)
[AMBER] Re: Marek Malý (Fri May 08 2009 - 14:12:39 CDT)
[AMBER] Can I use only a single point calculation to derive RESP charges? Josmar R. da Rocha (Fri May 08 2009 - 19:08:54 CDT)
- Re: [AMBER] Can I use only a single point calculation to derive RESP charges? FyD (Sat May 09 2009 - 01:00:36 CDT)
  - Re: [AMBER] Can I use only a single point calculation to derive RESP charges? Josmar R. da Rocha (Sat May 09 2009 - 10:19:07 CDT)
    - Re: [AMBER] Can I use only a single point calculation to derive RESP charges? FyD (Sun May 10 2009 - 01:52:12 CDT)
[AMBER] Modifying a water molecule Jorgen Simonsen (Sat May 09 2009 - 08:16:54 CDT)
[AMBER] AMBER 94 Charges for terminal LYN, GLH, ASH and CYM residues and some other unusual cases. todd_at_semichem.com (Sat May 09 2009 - 11:27:52 CDT)
- Re: [AMBER] AMBER 94 Charges for terminal LYN, GLH, ASH and CYM residues and some other unusual cases. Adrian Roitberg (Sat May 09 2009 - 13:07:08 CDT)
  - Re: [AMBER] AMBER 94 Charges for terminal LYN, GLH, ASH and CYM residues and some other unusual cases. todd_at_semichem.com (Sat May 09 2009 - 13:36:17 CDT)
    - Re: [AMBER] AMBER 94 Charges for terminal LYN, GLH, ASH and CYM residues and some other unusual cases. FyD (Sun May 10 2009 - 00:49:55 CDT)
    - Re: [AMBER] AMBER 94 Charges for terminal LYN, GLH, ASH and CYM residues and some other unusual cases. todd_at_semichem.com (Sun May 10 2009 - 16:56:24 CDT)
[AMBER] molsurf and probe radius David Watson (Sat May 09 2009 - 12:32:43 CDT)
- Re: [AMBER] molsurf and probe radius David A. Case (Mon May 11 2009 - 10:03:10 CDT)
[AMBER] xleap, mac number problem Mark M Huntress (Sat May 09 2009 - 14:46:46 CDT)
- [AMBER] RE: xleap, mac number problem Mark M Huntress (Sat May 09 2009 - 17:29:50 CDT)
[AMBER] please help me out Nancy (Sun May 10 2009 - 02:56:33 CDT)
- Re: [AMBER] please help me out FyD (Mon Mar 09 2009 - 05:05:06 CDT)
  - Re: [AMBER] please help me out bharat lakhani (Thu Mar 12 2009 - 01:04:00 CDT)
- Re: [AMBER] please help me out Wei Zhang (Sun May 10 2009 - 08:21:06 CDT)
[AMBER] MM-PBSA statistics Musa Ozboyaci (Sun May 10 2009 - 05:00:19 CDT)
[AMBER] The resonable way to create single strand DNA with NAB ? Marek Malý (Sun May 10 2009 - 12:12:09 CDT)
- Re: [AMBER] The resonable way to create single strand DNA with NAB ? David A. Case (Mon May 11 2009 - 06:34:16 CDT)
  - Re: [AMBER] The resonable way to create single strand DNA with NAB ? Marek Malý (Mon May 11 2009 - 07:18:06 CDT)
[AMBER] building quadruplex with NAB Peter Varnai (Sun May 10 2009 - 18:27:38 CDT)
- Re: [AMBER] building quadruplex with NAB David A. Case (Wed May 13 2009 - 06:48:38 CDT)
  - Re: [AMBER] building quadruplex with NAB Peter Varnai (Tue Oct 27 2009 - 15:00:09 CDT)
    - Re: [AMBER] building quadruplex with NAB case (Tue Oct 27 2009 - 21:23:29 CDT)
[AMBER] Adding non standard residues Jorgen Simonsen (Mon May 11 2009 - 03:54:25 CDT)
- Re: [AMBER] Adding non standard residues David A. Case (Mon May 11 2009 - 12:30:56 CDT)
  - Re: [AMBER] Adding non standard residues Jorgen Simonsen (Mon May 11 2009 - 16:11:49 CDT)
[AMBER] molecular crystal simulation Simona Irrera (Tue May 12 2009 - 06:04:26 CDT)
- Re: [AMBER] molecular crystal simulation David A. Case (Wed May 13 2009 - 17:28:37 CDT)
[AMBER] ptraj netcdf Bala subramanian (Tue May 12 2009 - 07:04:00 CDT)
- Re: [AMBER] ptraj netcdf Chris Moth (Tue May 12 2009 - 10:46:31 CDT)
  - [AMBER] anal output: Entalphy or Free Energy? E.M. (Tue May 12 2009 - 17:25:41 CDT)
[AMBER] anal output: Entalphy or Free Energy? Edward M (Tue May 12 2009 - 19:14:37 CDT)
[AMBER] Question about Thermal Integration with Softcore Elodie Laine (Wed May 13 2009 - 04:13:22 CDT)
- Re: [AMBER] Question about Thermal Integration with Softcore steinbrt_at_rci.rutgers.edu (Wed May 13 2009 - 10:11:16 CDT)
[AMBER] amber9 in fedora10 Bala subramanian (Wed May 13 2009 - 04:50:25 CDT)
- RE: [AMBER] amber9 in fedora10 Ross Walker (Wed May 13 2009 - 18:22:20 CDT)
[AMBER] essential dynamics Chunliyan (Wed May 13 2009 - 11:23:23 CDT)
- Re: [AMBER] essential dynamics David A. Case (Wed May 13 2009 - 12:15:50 CDT)
[AMBER] re: essential dynamics Chunliyan (Wed May 13 2009 - 12:25:57 CDT)
- Re: [AMBER] re: essential dynamics David A. Case (Wed May 13 2009 - 12:48:42 CDT)
  - RE: [AMBER] re: essential dynamics Niel Henriksen (Wed May 13 2009 - 13:28:22 CDT)
[AMBER] normal modes calculation Neha Gandhi (Wed May 13 2009 - 22:12:13 CDT)
- Re: [AMBER] normal modes calculation chaitanya koppisetty (Thu May 14 2009 - 03:51:28 CDT)
[AMBER] Amber - Leap- SolvateBox help Shubhra Gupta (Thu May 14 2009 - 00:04:16 CDT)
- RE: [AMBER] Amber - Leap- SolvateBox help Ross Walker (Thu May 14 2009 - 07:28:36 CDT)
- Re: [AMBER] Amber - Leap- SolvateBox help David A. Case (Fri May 15 2009 - 18:57:00 CDT)
- Re: [AMBER] Amber - Leap- SolvateBox help Shubhra Gupta (Mon May 18 2009 - 22:54:23 CDT)
  - Re: [AMBER] Amber - Leap- SolvateBox help David A. Case (Tue May 19 2009 - 06:48:39 CDT)
- Re: [AMBER] Amber - Leap- SolvateBox help Remya S R (Tue May 19 2009 - 01:22:12 CDT)
- RE: [AMBER] Amber - Leap- SolvateBox help Ross Walker (Wed May 20 2009 - 00:20:50 CDT)
[AMBER] pmemd running very slow in amber10 Vijay Manickam Achari (Thu May 14 2009 - 00:41:40 CDT)
- Re: [AMBER] pmemd running very slow in amber10 Carlos Simmerling (Thu May 14 2009 - 05:09:11 CDT)
  - RE: [AMBER] pmemd running very slow in amber10 Ross Walker (Thu May 14 2009 - 07:57:43 CDT)
- Re: [AMBER] pmemd running very slow in amber10 Robert Duke (Thu May 14 2009 - 08:38:29 CDT)
Re: [OFFLIST] Re: [AMBER] amber9 in fedora10 Bala subramanian (Thu May 14 2009 - 03:18:07 CDT)
[AMBER] MM-PBSA tutorial Workalemhu Berhanu (Thu May 14 2009 - 12:16:55 CDT)
- Re: [AMBER] MM-PBSA tutorial steinbrt_at_rci.rutgers.edu (Thu May 14 2009 - 12:26:50 CDT)
  - Re: [AMBER] MM-PBSA tutorial Cihan Aydin (Thu May 14 2009 - 20:19:04 CDT)
- Re: [AMBER] MM-PBSA tutorial Workalemhu Berhanu (Thu May 14 2009 - 13:53:25 CDT)
[AMBER] xmin Peter Varnai (Thu May 14 2009 - 16:29:09 CDT)
- Re: [AMBER] xmin Scott Brozell (Sun May 17 2009 - 15:45:27 CDT)
  - [AMBER] What is the purpose to do the bond constraints? Chih-Ying Lin (Sun May 17 2009 - 17:09:04 CDT)
  - Re: [AMBER] xmin Peter Varnai (Sun May 17 2009 - 19:58:00 CDT)
    - Re: [AMBER] xmin Scott Brozell (Mon May 18 2009 - 15:30:17 CDT)
[AMBER] Fw: MM-PBSA with explicit water mathew k varghese (Fri May 15 2009 - 01:43:46 CDT)
[AMBER] MM-PBSA with explicit water mathew k varghese (Fri May 15 2009 - 01:45:23 CDT)
[AMBER] xleap reading hydrogens giving error Jorgen Simonsen (Fri May 15 2009 - 02:47:10 CDT)
- Re: [AMBER] xleap reading hydrogens giving error David A. Case (Fri May 15 2009 - 09:17:04 CDT)
  - Re: [AMBER] xleap reading hydrogens giving error Jorgen Simonsen (Fri May 15 2009 - 10:54:17 CDT)
    - Re: [AMBER] xleap reading hydrogens giving error David A. Case (Fri May 15 2009 - 11:25:11 CDT)
    - [AMBER] how to make the different/specific displacement of ligand around protein? Chih-Ying Lin (Fri May 15 2009 - 18:55:49 CDT)
[AMBER] scee term Neha Gandhi (Fri May 15 2009 - 04:03:48 CDT)
- RE: [AMBER] scee term Ross Walker (Fri May 15 2009 - 10:02:09 CDT)
[AMBER] adding a standard amino acid as ligand sheerychen (Fri May 15 2009 - 04:37:51 CDT)
- Re: [AMBER] adding a standard amino acid as ligand FyD (Fri May 15 2009 - 08:39:18 CDT)
[AMBER] secstruct with ptraj Bala subramanian (Fri May 15 2009 - 05:19:54 CDT)
[AMBER] Issue related to vector saving S.Sundar Raman (Fri May 15 2009 - 08:35:01 CDT)
[AMBER] MM-GBSA energy decomposition and pairwise decomposition question Dong Xu (Fri May 15 2009 - 17:05:52 CDT)
[AMBER] FE: unexpected coordination 4 - using nonstandard tree type '4' ben rodriguez (Fri May 15 2009 - 17:09:44 CDT)
- Re: [AMBER] FE: unexpected coordination 4 - using nonstandard tree type '4' David A. Case (Fri May 15 2009 - 18:56:34 CDT)
[AMBER] Alignment of small molecule on peptide fragment Workalemhu Berhanu (Sat May 16 2009 - 04:31:08 CDT)
[AMBER] Alignment of small molecule on peptide fragment Workalemhu Berhanu (Sat May 16 2009 - 04:32:38 CDT)
[AMBER] Issue related to saving the vector in ptraj S.Sundar Raman (Sat May 16 2009 - 07:41:10 CDT)
- [AMBER] How to setup the pH value? Chih-Ying Lin (Sat May 16 2009 - 12:29:21 CDT)
  - Re: [AMBER] How to setup the pH value? David A. Case (Tue May 19 2009 - 14:08:53 CDT)
    - [AMBER] What are the elements to speed up the simulation? Chih-Ying Lin (Tue May 19 2009 - 17:17:07 CDT)
[AMBER] Amber 10 install parallel problem Hopkins, Robert (Sat May 16 2009 - 19:38:16 CDT)
[AMBER] Running PTRAJ command line scripts in background Hopkins, Robert (Sat May 16 2009 - 19:47:38 CDT)
- Re: [AMBER] Running PTRAJ command line scripts in background Jia Xu (Sun May 17 2009 - 02:16:49 CDT)
  - RE: [AMBER] Running PTRAJ command line scripts in background Hopkins, Robert (Sun May 17 2009 - 11:55:48 CDT)
- RE: [AMBER] Running PTRAJ command line scripts in background Ross Walker (Sun May 17 2009 - 22:35:09 CDT)
  - RE: [AMBER] Running PTRAJ command line scripts in background Hopkins, Robert (Mon May 18 2009 - 17:50:06 CDT)
[AMBER] makeDIST_RST: no map function for ambiguous restraint Peter Varnai (Sun May 17 2009 - 13:41:24 CDT)
- Re: [AMBER] makeDIST_RST: no map function for ambiguous restraint David A. Case (Tue May 19 2009 - 07:35:31 CDT)
  - Re: [AMBER] makeDIST_RST: no map function for ambiguous restraint Peter Varnai (Mon Jun 01 2009 - 14:49:36 CDT)
[AMBER] parallel amber on cluster Siavoush Dastmalchi (Mon May 18 2009 - 01:04:58 CDT)
- Re: [AMBER] parallel amber on cluster David A. Case (Mon May 18 2009 - 06:54:18 CDT)
[AMBER] Problem in Nmode Kshatresh Dutta Dubey (Mon May 18 2009 - 01:07:52 CDT)
[AMBER] Modification of His Jorgen Simonsen (Mon May 18 2009 - 05:51:50 CDT)
- Re: [AMBER] Modification of His David A. Case (Mon May 18 2009 - 06:58:34 CDT)
  - Re: [AMBER] Modification of His Jorgen Simonsen (Mon May 18 2009 - 07:16:10 CDT)
    - Re: [AMBER] Modification of His David A. Case (Mon May 18 2009 - 07:31:33 CDT)
- Re: [AMBER] Modification of His Bill Ross (Mon May 18 2009 - 15:06:16 CDT)
[AMBER] Error running MM _PBSA.pl script Vikas Sharma (Mon May 18 2009 - 07:00:13 CDT)
- å›žå¤ï¼š [AMBER] Error running MM _PBSA.pl script å»–é’åŽ (Mon May 18 2009 - 07:08:47 CDT)
  - Re: å›žå¤ï¼š [AMBER] Error running MM _PBSA.pl script Vikas Sharma (Mon May 18 2009 - 09:06:49 CDT)
    - å›žå¤ï¼š å›žå¤ï¼š [AMBER] Error running MM _PBSA.pl script å»–é’åŽ (Mon May 18 2009 - 09:41:14 CDT)
- RE: [AMBER] Error running MM _PBSA.pl script Ray Luo (Mon May 18 2009 - 12:43:30 CDT)
  - Re: [AMBER] Error running MM _PBSA.pl script Vikas Sharma (Mon May 18 2009 - 23:34:18 CDT)
    - Re: [AMBER] Error running MM _PBSA.pl script liuhui (Tue May 19 2009 - 09:29:23 CDT)
- Re: [AMBER] Error running MM _PBSA.pl script Vikas Sharma (Tue May 19 2009 - 10:02:21 CDT)
  - Re: [AMBER] Error running MM _PBSA.pl script liuhui (Tue May 19 2009 - 11:15:24 CDT)
[AMBER] problem with parmchk rebeca (Mon May 18 2009 - 08:59:51 CDT)
- Re: [AMBER] problem with parmchk David A. Case (Mon May 18 2009 - 09:19:54 CDT)
  - Re: [AMBER] problem with parmchk rebeca (Mon May 18 2009 - 09:34:31 CDT)
    - Re: [AMBER] problem with parmchk David A. Case (Mon May 18 2009 - 15:00:07 CDT)
[AMBER] no equilibrium Nancy (Mon May 18 2009 - 21:32:01 CDT)
[AMBER] no equilibrium Nancy (Mon May 18 2009 - 21:44:03 CDT)
- Re: [AMBER] no equilibrium steinbrt_at_rci.rutgers.edu (Mon May 18 2009 - 22:00:40 CDT)
[AMBER] The largest AMBER calculation(s)? Vlad (Mon May 18 2009 - 21:58:27 CDT)
[AMBER] Problem with Nmode Kshatresh Dutta Dubey (Mon May 18 2009 - 23:25:05 CDT)
- Re: [AMBER] Problem with Nmode David A. Case (Wed May 20 2009 - 13:02:44 CDT)
  - Re: [AMBER] Problem with Nmode Kshatresh Dutta Dubey (Thu May 21 2009 - 00:14:50 CDT)
    - Re: [AMBER] Problem with Nmode David A. Case (Thu May 21 2009 - 07:29:06 CDT)
[AMBER] AMBER 10 output Sergey Samsonov (Tue May 19 2009 - 02:33:21 CDT)
- Re: [AMBER] AMBER 10 output steinbrt_at_rci.rutgers.edu (Tue May 19 2009 - 08:53:03 CDT)
  - Re: [AMBER] AMBER 10 output Sergey Samsonov (Tue May 19 2009 - 09:53:41 CDT)
[AMBER] Problem with nonstandard residues moitrayee_at_mbu.iisc.ernet.in (Tue May 19 2009 - 06:48:33 CDT)
- Re: [AMBER] Problem with nonstandard residues David A. Case (Tue May 19 2009 - 07:54:14 CDT)
  - Re: [AMBER] Problem with nonstandard residues moitrayee_at_mbu.iisc.ernet.in (Tue May 19 2009 - 08:10:00 CDT)
    - Re: [AMBER] Problem with nonstandard residues David A. Case (Tue May 19 2009 - 10:22:15 CDT)
    - Re: [AMBER] Problem with nonstandard residues moitrayee_at_mbu.iisc.ernet.in (Tue May 19 2009 - 11:47:38 CDT)
[AMBER] gaff and aromatic compounds rebeca (Tue May 19 2009 - 10:50:02 CDT)
- Re: [AMBER] gaff and aromatic compounds David A. Case (Tue May 19 2009 - 11:07:29 CDT)
- Re: [AMBER] gaff and aromatic compounds Junmei Wang (Thu May 21 2009 - 20:24:52 CDT)
  - Re: [AMBER] gaff and aromatic compounds rebeca (Fri May 22 2009 - 04:04:45 CDT)
    - Re: [AMBER] gaff and aromatic compounds Junmei Wang (Tue May 26 2009 - 11:03:53 CDT)
[AMBER] loadpdb atom type Mark M Huntress (Tue May 19 2009 - 11:20:20 CDT)
- Re: [AMBER] loadpdb atom type Carlos Simmerling (Tue May 19 2009 - 12:09:29 CDT)
  - RE: [AMBER] loadpdb atom type Mark M Huntress (Tue May 19 2009 - 13:15:02 CDT)
- Re: [AMBER] loadpdb atom type David A. Case (Tue May 19 2009 - 13:19:44 CDT)
[AMBER] Tutorial A1 Workalemhu Berhanu (Tue May 19 2009 - 18:05:15 CDT)
[AMBER] resp charge R. A. (Tue May 19 2009 - 21:35:25 CDT)
- [AMBER] resp charge FyD (Wed May 20 2009 - 02:42:07 CDT)
- RE: [AMBER] resp charge Ross Walker (Wed May 20 2009 - 10:05:20 CDT)
[AMBER] gaff and aromatic compounds rebeca (Wed May 20 2009 - 03:54:43 CDT)
- Re: [AMBER] gaff and aromatic compounds David A. Case (Wed May 20 2009 - 07:04:05 CDT)
[AMBER] MM PBSA output Vikas Sharma (Wed May 20 2009 - 06:53:57 CDT)
- å›žå¤ï¼š [AMBER] MM PBSA output å»–é’åŽ (Wed May 20 2009 - 07:15:04 CDT)
  - Re: å›žå¤ï¼š [AMBER] MM PBSA output Vikas Sharma (Wed May 20 2009 - 12:54:32 CDT)
[AMBER] Amber/CHARMM summer school David A. Case (Wed May 20 2009 - 07:40:39 CDT)
- RE: [AMBER] Amber/CHARMM summer school CHAMI F. (Thu May 21 2009 - 06:56:23 CDT)
[AMBER] ptraj questions Jia Xu (Wed May 20 2009 - 09:39:13 CDT)
- Re: [AMBER] ptraj questions Myunggi Yi (Fri May 22 2009 - 08:57:08 CDT)
  - Re: [AMBER] ptraj questions Jia Xu (Sun May 24 2009 - 00:06:10 CDT)
[AMBER] RE: add magnesium Ross Walker (Wed May 20 2009 - 16:30:09 CDT)
[AMBER] how to use two dimensions periodic boundary ? Nancy (Wed May 20 2009 - 20:32:50 CDT)
[AMBER] errors when add ions zgong.hust (Wed May 20 2009 - 21:51:48 CDT)
- Re: [AMBER] errors when add ions David A. Case (Thu May 21 2009 - 07:23:08 CDT)
- [AMBER] Why does protein carry charges? Chih-Ying Lin (Fri May 22 2009 - 23:09:21 CDT)
  - [AMBER] How to choose the counter ions for proteins? Chih-Ying Lin (Sat May 23 2009 - 00:42:40 CDT)
    - RE: [AMBER] How to choose the counter ions for proteins? Ross Walker (Sat May 23 2009 - 13:09:27 CDT)
    - Re: RE: [AMBER] How to choose the counter ions for proteins? Chih-Ying Lin (Sat May 23 2009 - 13:16:49 CDT)
  - RE: [AMBER] Why does protein carry charges? Ross Walker (Sat May 23 2009 - 13:06:57 CDT)
[AMBER] Protein with HETATM, am I doing the nicholus bhattacharjee (Wed May 20 2009 - 23:48:42 CDT)
- Re: [AMBER] Protein with HETATM, am I doing the Amit Bajaj (Thu May 21 2009 - 00:26:49 CDT)
  - Re: [AMBER] Protein with HETATM, am I doing the nicholus bhattacharjee (Thu May 21 2009 - 01:43:37 CDT)
    - Re: [AMBER] Protein with HETATM, am I doing the amit (Mon May 25 2009 - 10:26:15 CDT)
[AMBER] Radius for Bromine in MMPBSA calculation john smith (Thu May 21 2009 - 00:24:05 CDT)
- RE: [AMBER] Radius for Bromine in MMPBSA calculation Ray Luo (Thu May 21 2009 - 11:32:41 CDT)
  - Re: [AMBER] Radius for Bromine in MMPBSA calculation john smith (Sun May 24 2009 - 23:52:48 CDT)
[AMBER] Protein with HETATM, am I doing the right thing nicholus bhattacharjee (Thu May 21 2009 - 06:21:15 CDT)
- Re: [AMBER] Protein with HETATM, am I doing the right thing David A. Case (Thu May 21 2009 - 07:39:14 CDT)
  - Re: [AMBER] Protein with HETATM, am I doing the right thing nicholus bhattacharjee (Thu May 21 2009 - 11:28:52 CDT)
[AMBER] Loading PDB of complex Vikas Sharma (Thu May 21 2009 - 08:13:36 CDT)
- Re: [AMBER] Loading PDB of complex Carlos Simmerling (Thu May 21 2009 - 08:48:06 CDT)
  - Re: [AMBER] Loading PDB of complex Vikas Sharma (Fri May 22 2009 - 00:56:36 CDT)
[AMBER] Installation directory Thomas Spraggins (Thu May 21 2009 - 13:02:59 CDT)
- Re: [AMBER] Installation directory David A. Case (Thu May 21 2009 - 13:19:28 CDT)
  - Re: [AMBER] Installation directory Thomas Spraggins (Thu May 21 2009 - 14:18:13 CDT)
    - Re: [AMBER] Installation directory Atro Tossavainen (Mon May 25 2009 - 03:10:34 CDT)
[AMBER] Segmentation error in Ptraj Kshatresh Dutta Dubey (Fri May 22 2009 - 02:17:27 CDT)
[AMBER] lipid membrane(dppc) in amber xueqin pang (Fri May 22 2009 - 03:42:54 CDT)
- Re: [AMBER] lipid membrane(dppc) in amber Myunggi Yi (Fri May 22 2009 - 08:45:20 CDT)
[AMBER] lipid membrane(dppc) in amber xueqin pang (Fri May 22 2009 - 04:01:26 CDT)
[AMBER] decomposition and alanine scanning å»–é’åŽ (Fri May 22 2009 - 09:13:49 CDT)
[AMBER] MMPBSA extract coordinate vijayaraj_at_clri.res.in (Fri May 22 2009 - 13:00:57 CDT)
[AMBER] Nab units ? Marek Maly (Fri May 22 2009 - 19:20:14 CDT)
- Re: [AMBER] Nab units ? David A. Case (Fri May 22 2009 - 20:33:34 CDT)
  - Re: [AMBER] Nab units ? Marek Maly (Fri May 22 2009 - 20:43:41 CDT)
[AMBER] 2 atoms not in residue template Workalemhu Berhanu (Sat May 23 2009 - 19:11:12 CDT)
[AMBER] file contains 2 atoms not in residue templates Workalemhu Berhanu (Sat May 23 2009 - 19:17:09 CDT)
- Re: [AMBER] file contains 2 atoms not in residue templates David A. Case (Sun May 24 2009 - 08:12:14 CDT)
[AMBER] problem with MM-PBSA Maryam Hamzehee (Sat May 23 2009 - 23:48:05 CDT)
[AMBER] nanoseconds of simulation with nscm=0 Naser Alijabbari (Sun May 24 2009 - 12:20:18 CDT)
- Re: [AMBER] nanoseconds of simulation with nscm=0 Thomas Cheatham (Sun May 24 2009 - 13:27:33 CDT)
  - Re: [AMBER] nanoseconds of simulation with nscm=0 Naser Alijabbari (Sun May 24 2009 - 14:56:28 CDT)
    - Re: [AMBER] nanoseconds of simulation with nscm=0 Thomas Cheatham (Sun May 24 2009 - 15:37:23 CDT)
[AMBER] Unit 8 Error on OPEN: prmtop Workalemhu Berhanu (Sun May 24 2009 - 12:27:38 CDT)
- Re: [AMBER] Unit 8 Error on OPEN: prmtop Peter Gannett (Sun May 24 2009 - 12:46:47 CDT)
- Re: [AMBER] Unit 8 Error on OPEN: prmtop Alessandro Nascimento (Sun May 24 2009 - 13:28:26 CDT)
  - Re: [AMBER] Unit 8 Error on OPEN: prmtop Peter Gannett (Sun May 24 2009 - 14:29:58 CDT)
  - Re: [AMBER] Unit 8 Error on OPEN: prmtop Workalemhu Berhanu (Sun May 24 2009 - 17:12:00 CDT)
[AMBER] Strange high temperature in softcore TI Tom Joseph (Sun May 24 2009 - 20:54:43 CDT)
- Re: [AMBER] Strange high temperature in softcore TI steinbrt_at_rci.rutgers.edu (Sun May 24 2009 - 21:26:28 CDT)
  - Re: [AMBER] Strange high temperature in softcore TI Tom Joseph (Sun May 24 2009 - 22:20:20 CDT)
    - Re: [AMBER] Strange high temperature in softcore TI steinbrt_at_rci.rutgers.edu (Sun May 24 2009 - 23:13:38 CDT)
[AMBER] How to know that the md is stable in equilibration run nicholus bhattacharjee (Mon May 25 2009 - 06:54:25 CDT)
- [AMBER] Re: How to know that the md is stable in equilibration run nicholus bhattacharjee (Mon May 25 2009 - 11:11:39 CDT)
[AMBER] Problem with MM-PBSA energy calculation Rubben Torella (Mon May 25 2009 - 10:58:41 CDT)
- Re: [AMBER] Problem with MM-PBSA energy calculation Barbault Florent (Mon May 25 2009 - 13:57:19 CDT)
  - Re: [AMBER] Problem with MM-PBSA energy calculation Rubben Torella (Tue May 26 2009 - 06:24:56 CDT)
[AMBER] hbond_ptraj balaji nagarajan (Mon May 25 2009 - 15:05:12 CDT)
- Re: [AMBER] hbond_ptraj Thomas Cheatham (Wed May 27 2009 - 19:39:15 CDT)
[AMBER] Question about &dipoles printing in AMBER 8 Karen Callahan (Mon May 25 2009 - 18:46:00 CDT)
[AMBER] partial charge and topology of intrastrand cross-link DNA Shuang Ding (Mon May 25 2009 - 21:27:43 CDT)
- Re: [AMBER] partial charge and topology of intrastrand cross-link DNA FyD (Wed May 27 2009 - 00:27:40 CDT)
[AMBER] problem with MM-PBSA Maryam Hamzehee (Mon May 25 2009 - 23:52:29 CDT)
- Re: [AMBER] problem with MM-PBSA David A. Case (Tue May 26 2009 - 06:37:31 CDT)
- RE: [AMBER] problem with MM-PBSA Ray Luo (Tue May 26 2009 - 11:44:14 CDT)
- Re: [AMBER] problem with MM-PBSA Thomas Cheatham (Wed May 27 2009 - 19:35:30 CDT)
- Re: [AMBER] problem with MM-PBSA Bill Ross (Wed May 27 2009 - 19:52:19 CDT)
[AMBER] Molecular simulation of a protein using special H2O cluster Rilei Yu (Tue May 26 2009 - 03:20:56 CDT)
- Re: [AMBER] Molecular simulation of a protein using special H2O cluster Carlos Simmerling (Tue May 26 2009 - 06:45:50 CDT)
- Re: [AMBER] Molecular simulation of a protein using special H2O cluster Rilei Yu (Tue May 26 2009 - 19:21:15 CDT)
  - Re: [AMBER] Molecular simulation of a protein using special H2O cluster Carlos Simmerling (Tue May 26 2009 - 19:25:03 CDT)
[AMBER] Re: About Amber installations Alan (Tue May 26 2009 - 04:53:37 CDT)
- Re: [AMBER] Re: About Amber installations jacky zhao (Tue May 26 2009 - 06:18:25 CDT)
[AMBER] ligand QM/semi-empirical coords optmisation Alan (Tue May 26 2009 - 05:55:09 CDT)
- Re: [AMBER] ligand QM/semi-empirical coords optmisation David A. Case (Tue May 26 2009 - 06:41:25 CDT)
  - Re: [AMBER] ligand QM/semi-empirical coords optmisation Alan (Thu Jun 04 2009 - 09:19:28 CDT)
    - Re: [AMBER] ligand QM/semi-empirical coords optmisation David A. Case (Thu Jun 04 2009 - 10:06:28 CDT)
    - Re: [AMBER] ligand QM/semi-empirical coords optmisation Alan (Thu Jun 04 2009 - 13:05:27 CDT)
  - Re: [AMBER] ligand QM/semi-empirical coords optmisation Junmei Wang (Fri Jun 05 2009 - 10:01:32 CDT)
    - Re: [AMBER] ligand QM/semi-empirical coords optmisation Francesco Pietra (Fri Jun 05 2009 - 13:17:45 CDT)
[AMBER] problem with program anal within Amber10 Marina Grabar (Tue May 26 2009 - 06:48:38 CDT)
- Re: [AMBER] problem with program anal within Amber10 David A. Case (Tue May 26 2009 - 07:03:01 CDT)
[AMBER] partial charges of lipid membrane for GPCR system xueqin pang (Tue May 26 2009 - 08:34:34 CDT)
[AMBER] mdfil: Error unknown flag during sander minimization Workalemhu Berhanu (Tue May 26 2009 - 08:57:29 CDT)
- Re: [AMBER] mdfil: Error unknown flag during sander minimization David A. Case (Tue May 26 2009 - 09:05:37 CDT)
- Re: [AMBER] mdfil: Error unknown flag during sander minimization Shubhra Gupta (Tue May 26 2009 - 23:07:25 CDT)
[AMBER] RE: About Amber10 installation "Possible Failure" Ross Walker (Tue May 26 2009 - 10:38:19 CDT)
[AMBER] get typeid of -1, sleap - AMBER with amoeba ff Tomasio, Susana (Tue May 26 2009 - 10:51:18 CDT)
[AMBER] Tutorial 4 Please check the total charge and your -nc flag Workalemhu Berhanu (Tue May 26 2009 - 14:47:07 CDT)
- Re: [AMBER] Tutorial 4 Please check the total charge and your -nc flag David A. Case (Wed May 27 2009 - 06:42:29 CDT)
[AMBER] FATAL error in creating topology and coordinate files for organic molecules with Antechamber Workalemhu Berhanu (Tue May 26 2009 - 16:45:55 CDT)
- Re: [AMBER] FATAL error in creating topology and coordinate files for organic molecules with Antechamber Rubben Torella (Tue May 26 2009 - 17:33:18 CDT)
[AMBER] Re: Help with xleap Taufik Al-Sarraj (Tue May 26 2009 - 18:58:00 CDT)
[AMBER] ACE residue - amoeba_amino.off and amoeba_aminont.off - different labels Tomasio, Susana (Wed May 27 2009 - 06:25:35 CDT)
- Re: [AMBER] ACE residue - amoeba_amino.off and amoeba_aminont.off - different labels David A. Case (Wed May 27 2009 - 06:57:07 CDT)
  - RE: [AMBER] ACE residue - amoeba_amino.off and amoeba_aminont.off- different labels Tomasio, Susana (Wed May 27 2009 - 07:13:58 CDT)
[AMBER] PARMCAL calculation ? Marek Maly (Wed May 27 2009 - 09:19:48 CDT)
[AMBER] MM-PBSA and NetCDF Bradshaw, Richard (Wed May 27 2009 - 10:38:13 CDT)
[AMBER] Tutorial 4 Parameter file was not saved Workalemhu Berhanu (Wed May 27 2009 - 11:00:30 CDT)
- RE: [AMBER] Tutorial 4 Parameter file was not saved Ross Walker (Wed May 27 2009 - 12:31:30 CDT)
[AMBER] heating advice Mark M Huntress (Wed May 27 2009 - 15:44:26 CDT)
[AMBER] SANDER BOMB PRADEEP VENKATARAMAN (Wed May 27 2009 - 21:39:56 CDT)
- Re: [AMBER] SANDER BOMB David A. Case (Thu May 28 2009 - 09:29:50 CDT)
[AMBER] Changing bond length manoj singh (Wed May 27 2009 - 22:47:52 CDT)
- RE: [AMBER] Changing bond length Ross Walker (Wed May 27 2009 - 23:38:59 CDT)
  - Re: [AMBER] Changing bond length manoj singh (Thu May 28 2009 - 12:00:14 CDT)
[AMBER] AMOEBA and carbon nanotubes + include parameters Tomasio, Susana (Thu May 28 2009 - 05:23:00 CDT)
[AMBER] MM-PBSA nmode statistics Dmitry Osolodkin (Thu May 28 2009 - 06:54:18 CDT)
- Re: [AMBER] MM-PBSA nmode statistics Kshatresh Dutta Dubey (Fri May 29 2009 - 00:13:34 CDT)
  - Re: [AMBER] MM-PBSA nmode statistics Dmitry Osolodkin (Fri May 29 2009 - 05:53:27 CDT)
[AMBER] contacts in ptraj Å·ÑôµÂ·½ (Thu May 28 2009 - 06:55:28 CDT)
[AMBER] how to know that adequate equilibration from rmsd curve of equilibration nicholus bhattacharjee (Thu May 28 2009 - 08:37:29 CDT)
[AMBER] FW: About Amber10 installation "Possible Failure" Ross Walker (Thu May 28 2009 - 09:06:31 CDT)
[AMBER] Minimization error on protonated system? Please help. Thanks! Haizhen Zhong (Thu May 28 2009 - 09:58:49 CDT)
- Re: [AMBER] Minimization error on protonated system? Please help. Thanks! David A. Case (Thu May 28 2009 - 10:17:59 CDT)
[AMBER] Minimization on MM-PBSA Rubben Torella (Thu May 28 2009 - 10:23:07 CDT)
Re: [AMBER] how to know that adequate equilibration from rmsd curve of equilibration Bill Ross (Thu May 28 2009 - 10:42:13 CDT)
- Re: [AMBER] how to know that adequate equilibration from rmsd curve of equilibration nicholus bhattacharjee (Thu May 28 2009 - 13:08:52 CDT)
  - Re: [AMBER] how to know that adequate equilibration from rmsd curve of equilibration Carlos Simmerling (Thu May 28 2009 - 13:15:09 CDT)
[AMBER] unnatural amino acid emiliawu_at_dicp.ac.cn (Fri May 29 2009 - 01:56:43 CDT)
- Re: [AMBER] unnatural amino acid FyD (Thu May 28 2009 - 13:46:27 CDT)
[AMBER] xleap segmentation fault Jayalakshmi Sridhar (Thu May 28 2009 - 11:29:47 CDT)
- Re: [AMBER] xleap segmentation fault David A. Case (Thu May 28 2009 - 15:05:12 CDT)
- Re: [AMBER] xleap segmentation fault Jayalakshmi Sridhar (Fri May 29 2009 - 10:45:25 CDT)
[AMBER] ask for parm99MOD xiaoqin huang (Thu May 28 2009 - 13:16:35 CDT)
- RE: [AMBER] ask for parm99MOD xiaoqin huang (Thu May 28 2009 - 14:31:14 CDT)
  - Re: [AMBER] ask for parm99MOD Adrian Roitberg (Thu May 28 2009 - 14:38:23 CDT)
RE: [AMBER] question of ibelly used in pmemd Kristina Furse (Mon Jul 20 2009 - 11:56:26 CDT)
- Re: [AMBER] question of ibelly used in pmemd Robert Duke (Mon Jul 20 2009 - 12:10:03 CDT)
- RE: [AMBER] question of ibelly used in pmemd xiaoqin huang (Mon Jul 20 2009 - 12:20:36 CDT)
  - RE: [AMBER] question of ibelly used in pmemd Ross Walker (Mon Jul 20 2009 - 12:32:08 CDT)
    - RE: [AMBER] question of ibelly used in pmemd xiaoqin huang (Mon Jul 20 2009 - 12:39:16 CDT)
    - Re: [AMBER] question of ibelly used in pmemd Robert Duke (Mon Jul 20 2009 - 12:55:23 CDT)
  - Re: [AMBER] question of ibelly used in pmemd Robert Duke (Tue Jul 21 2009 - 08:15:20 CDT)
RE: [AMBER] question of ibelly used in pmemd Ross Walker (Wed Jul 15 2009 - 20:32:07 CDT)
- RE: [AMBER] question of ibelly used in pmemd xiaoqin huang (Fri Jul 17 2009 - 09:36:06 CDT)
[AMBER] How to take into account the charge in GAFF parameterization Workalemhu Berhanu (Thu May 28 2009 - 18:22:07 CDT)
- Re: [AMBER] How to take into account the charge in GAFF parameterization cgji (Fri May 29 2009 - 01:49:44 CDT)
[AMBER] J coupling constant calculation Neha Gandhi (Fri May 29 2009 - 00:24:37 CDT)
- Re: [AMBER] J coupling constant calculation Dechang Li (Fri May 29 2009 - 00:31:06 CDT)
- Re: [AMBER] J coupling constant calculation Gustavo Seabra (Tue Jun 02 2009 - 09:18:08 CDT)
[AMBER] broken Ligand Shubhra Gupta (Fri May 29 2009 - 08:28:22 CDT)
- Re: [AMBER] broken Ligand David A. Case (Fri May 29 2009 - 09:45:20 CDT)
  - Re: [AMBER] broken Ligand Shubhra Gupta (Sat May 30 2009 - 01:35:46 CDT)
    - Re: [AMBER] broken Ligand David A. Case (Sun May 31 2009 - 07:50:57 CDT)
[AMBER] QQD psuedoatom restraints Titus, Jamie (bairdje) (Fri May 29 2009 - 09:02:31 CDT)
- Re: [AMBER] QQD psuedoatom restraints David A. Case (Fri May 29 2009 - 10:18:29 CDT)
  - RE: [AMBER] QQD psuedoatom restraints Titus, Jamie (bairdje) (Fri May 29 2009 - 14:01:34 CDT)
    - Re: [AMBER] QQD psuedoatom restraints David A. Case (Fri May 29 2009 - 14:26:27 CDT)
    - RE: [AMBER] QQD psuedoatom restraints Titus, Jamie (bairdje) (Mon Jun 01 2009 - 06:21:19 CDT)
  - RE: [AMBER] QQD psuedoatom restraints Titus, Jamie (bairdje) (Fri Jun 12 2009 - 13:51:25 CDT)
    - Re: [AMBER] QQD psuedoatom restraints David A. Case (Mon Jun 15 2009 - 07:00:23 CDT)
[AMBER] Targeted MD and QM/MM Gabriel Urquiza (Fri May 29 2009 - 15:09:31 CDT)
- [AMBER] protein molecular weight? Chih-Ying Lin (Fri May 29 2009 - 17:44:24 CDT)
  - Re: [AMBER] protein molecular weight? Tom Joseph (Fri May 29 2009 - 18:40:58 CDT)
- Re: [AMBER] Targeted MD and QM/MM Gustavo Seabra (Tue Jun 02 2009 - 09:43:35 CDT)
  - Re: [AMBER] Targeted MD and QM/MM Gabriel Urquiza (Tue Jun 02 2009 - 17:08:11 CDT)
[AMBER] the atom number exceeds the MAXATOM, reallocate memory automatically Workalemhu Berhanu (Sat May 30 2009 - 06:20:03 CDT)
- Re: [AMBER] the atom number exceeds the MAXATOM, reallocate memory automatically David A. Case (Sat May 30 2009 - 08:11:59 CDT)
[AMBER] ERROR in ptrajInitializeState(): Attempting .... Siavoush Dastmalchi (Sat May 30 2009 - 11:06:51 CDT)
[AMBER] RE: ERROR in ptrajInitializeState(): Attempting .... Siavoush Dastmalchi (Sat May 30 2009 - 12:11:55 CDT)
[AMBER] Parameter file content manoj singh (Sat May 30 2009 - 20:53:37 CDT)
- Re: [AMBER] Parameter file content Tom Joseph (Sat May 30 2009 - 21:23:48 CDT)
[AMBER] create a simulation box Workalemhu Berhanu (Sat May 30 2009 - 22:06:24 CDT)
- Re: [AMBER] create a simulation box Gustavo Seabra (Tue Jun 02 2009 - 10:08:46 CDT)
[AMBER] can I get partial charge for lipid membrane with Antechamber and RESP xueqin pang (Sun May 31 2009 - 07:43:09 CDT)
- Re: [AMBER] can I get partial charge for lipid membrane with Antechamber and RESP FyD (Sun May 31 2009 - 07:51:50 CDT)
[AMBER] Can we use GROMACS or NAMD for MD, and then use MM-PBSA to culculate binding energy xueqin pang (Sun May 31 2009 - 07:47:57 CDT)
- Re: [AMBER] Can we use GROMACS or NAMD for MD, and then use MM-PBSA to culculate binding energy Gustavo Seabra (Tue Jun 02 2009 - 09:53:19 CDT)
- Re: [AMBER] Can we use GROMACS or NAMD for MD, and then use MM-PBSA to culculate binding energy Marc Baaden (Tue Jun 02 2009 - 15:56:29 CDT)
  - Re: [AMBER] Can we use GROMACS or NAMD for MD, and then use MM-PBSA to culculate binding energy jacky zhao (Wed Jun 03 2009 - 08:44:12 CDT)
[AMBER] solutes in a simulation box Workalemhu Berhanu (Sun May 31 2009 - 11:59:39 CDT)
[AMBER] Choice of force feild manoj singh (Sun May 31 2009 - 12:12:23 CDT)
- Re: [AMBER] Choice of force feild Gustavo Seabra (Tue Jun 02 2009 - 09:58:11 CDT)
[AMBER] Choice of force field manoj singh (Sun May 31 2009 - 15:39:13 CDT)
- Re: [AMBER] Choice of force field Carlos Simmerling (Mon Jun 01 2009 - 06:14:09 CDT)
[AMBER] sleap and delete FyD (Mon Jun 01 2009 - 02:35:32 CDT)
[AMBER] converting vibrational frequency aneesh cna (Mon Jun 01 2009 - 06:22:01 CDT)
- Re: [AMBER] converting vibrational frequency David A. Case (Mon Jun 01 2009 - 06:39:32 CDT)
  - Re: [AMBER] converting vibrational frequency aneesh cna (Mon Jun 01 2009 - 11:53:22 CDT)
[AMBER] atom number exceeds the MAXATOM when running antechamber xueqin pang (Mon Jun 01 2009 - 07:53:23 CDT)
- Re: [AMBER] atom number exceeds the MAXATOM when running antechamber Gustavo Seabra (Tue Jun 02 2009 - 10:04:33 CDT)
[AMBER] different comformations to choose for RESP xueqin pang (Mon Jun 01 2009 - 08:47:30 CDT)
- Re: [AMBER] different comformations to choose for RESP FyD (Mon Jun 01 2009 - 09:32:21 CDT)
[AMBER] hbond_DNAtraj balaji nagarajan (Mon Jun 01 2009 - 12:08:15 CDT)
- Re: [AMBER] hbond_DNAtraj Jianyin Shao (Wed Jun 03 2009 - 11:52:41 CDT)
[AMBER] minimization to reduce covalent deviation Peter Varnai (Mon Jun 01 2009 - 15:25:07 CDT)
- Re: [AMBER] minimization to reduce covalent deviation David A. Case (Tue Jun 02 2009 - 08:38:58 CDT)
[AMBER] how to choose different comformations for RESP xueqin pang (Mon Jun 01 2009 - 19:32:51 CDT)
- Re: [AMBER] how to choose different comformations for RESP cgji (Tue Jun 02 2009 - 00:14:02 CDT)
[AMBER] MMPBSA and mm_pbsa_statistics.pl error john smith (Tue Jun 02 2009 - 00:38:54 CDT)
- Re: [AMBER] MMPBSA and mm_pbsa_statistics.pl error Ray Luo (Tue Jun 02 2009 - 23:49:34 CDT)
[AMBER] how to add ions bharat lakhani (Tue Jun 02 2009 - 02:25:46 CDT)
[AMBER] Atom names Rose Tamil (Tue Jun 02 2009 - 05:53:50 CDT)
- Re: [AMBER] Atom names Carlos Simmerling (Tue Jun 02 2009 - 06:39:25 CDT)
- Re: [AMBER] Atom names David A. Case (Tue Jun 02 2009 - 06:44:39 CDT)
  - Re: [AMBER] Atom names Rose Tamil (Tue Jun 02 2009 - 06:50:47 CDT)
[AMBER] help with parameters for ions rebeca (Tue Jun 02 2009 - 07:46:14 CDT)
- Re: [AMBER] help with parameters for ions David A. Case (Tue Jun 02 2009 - 08:46:40 CDT)
  - Re: [AMBER] help with parameters for ions rebeca (Tue Jun 02 2009 - 10:10:17 CDT)
    - Re: [AMBER] help with parameters for ions InSuk Joung (Tue Jun 02 2009 - 10:28:55 CDT)
  - Re: [AMBER] help with parameters for ions rebeca (Tue Jun 02 2009 - 12:38:00 CDT)
    - Re: [AMBER] help with parameters for ions InSuk Joung (Tue Jun 02 2009 - 13:14:46 CDT)
[AMBER] Error in MM PBSA Vikas Sharma (Tue Jun 02 2009 - 08:42:16 CDT)
- Re: [AMBER] Error in MM PBSA David A. Case (Tue Jun 02 2009 - 09:05:09 CDT)
Fwd: Re: [AMBER] help with parameters for ions rebeca (Tue Jun 02 2009 - 13:33:41 CDT)
[AMBER] PARMSCAN alegil_at_fq.uh.cu (Tue Jun 02 2009 - 17:26:42 CDT)
[AMBER] PARMSCAN alegil_at_fq.uh.cu (Tue Jun 02 2009 - 17:41:54 CDT)
[AMBER] preparation of two solutes of organic molecules in a simulation box Workalemhu Berhanu (Tue Jun 02 2009 - 18:09:04 CDT)
[AMBER] addions Shubhra Gupta (Wed Jun 03 2009 - 00:47:11 CDT)
- [AMBER] Re: addions Shubhra Gupta (Wed Jun 03 2009 - 06:12:32 CDT)
  - Re: [AMBER] Re: addions nicholus bhattacharjee (Wed Jun 03 2009 - 08:44:51 CDT)
  - [AMBER] Re: addions Peter Gannett (Wed Jun 03 2009 - 09:17:57 CDT)
    - Re: [AMBER] Re: addions Shubhra Gupta (Thu Jun 04 2009 - 23:38:20 CDT)
[AMBER] Distance restraints between groups of atoms Germain Vallverdu (Wed Jun 03 2009 - 01:58:57 CDT)
- Re: [AMBER] Distance restraints between groups of atoms David A. Case (Wed Jun 03 2009 - 07:27:04 CDT)
  - [AMBER] AMBER10: error message mdfil flag..... Catein Catherine (Wed Jun 03 2009 - 09:14:50 CDT)
    - Re: [AMBER] AMBER10: error message mdfil flag..... David A. Case (Wed Jun 03 2009 - 09:30:08 CDT)
  - Re: [AMBER] Distance restraints between groups of atoms Germain Vallverdu (Wed Jun 03 2009 - 09:43:37 CDT)
[AMBER] use of random seed in multiple runs Andrew Voronkov (Wed Jun 03 2009 - 04:28:52 CDT)
- Re: [AMBER] use of random seed in multiple runs Carlos Simmerling (Wed Jun 03 2009 - 05:13:23 CDT)
  - Re: [AMBER] use of random seed in multiple runs Andrew Voronkov (Wed Jun 03 2009 - 12:00:32 CDT)
- Re: [AMBER] use of random seed in multiple runs Gustavo Seabra (Wed Jun 03 2009 - 08:55:24 CDT)
- Re: [AMBER] use of random seed in multiple runs Andrew Voronkov (Wed Jun 03 2009 - 14:26:48 CDT)
  - Re: [AMBER] use of random seed in multiple runs Gustavo Seabra (Wed Jun 03 2009 - 21:00:51 CDT)
[AMBER] only ff94 and ff99 for GBSA? Andrew Voronkov (Wed Jun 03 2009 - 05:28:15 CDT)
- Re: [AMBER] only ff94 and ff99 for GBSA? Carlos Simmerling (Wed Jun 03 2009 - 05:51:09 CDT)
- Re: [AMBER] only ff94 and ff99 for GBSA? Andrew Voronkov (Wed Jun 03 2009 - 06:52:13 CDT)
  - Re: [AMBER] only ff94 and ff99 for GBSA? David A. Case (Wed Jun 03 2009 - 07:24:56 CDT)
[AMBER] NO output when running espgen? xueqin pang (Wed Jun 03 2009 - 08:13:06 CDT)
[AMBER] Pentavalent Phosphorous and Antechamber Peterson, Matthew W. (Wed Jun 03 2009 - 09:12:44 CDT)
- Re: [AMBER] Pentavalent Phosphorous and Antechamber David A. Case (Wed Jun 03 2009 - 11:35:26 CDT)
- Re: [AMBER] Pentavalent Phosphorous and Antechamber Shubhra Gupta (Wed Jun 03 2009 - 23:37:08 CDT)
- Re: [AMBER] Pentavalent Phosphorous and Antechamber FyD (Thu Jun 04 2009 - 01:29:59 CDT)
[AMBER] spc.itp for the Amber force field rebeca (Wed Jun 03 2009 - 09:46:46 CDT)
- Re: [AMBER] spc.itp for the Amber force field Alan (Wed Jun 03 2009 - 10:38:56 CDT)
[AMBER] problems with EP of TIP4PEW rebeca (Wed Jun 03 2009 - 10:43:58 CDT)
- Re: [AMBER] problems with EP of TIP4PEW David A. Case (Wed Jun 03 2009 - 11:29:43 CDT)
  - Re: [AMBER] problems with EP of TIP4PEW rebeca (Wed Jun 03 2009 - 13:40:12 CDT)
[AMBER] creating bond Jorgen Simonsen (Wed Jun 03 2009 - 12:04:11 CDT)
- Re: [AMBER] creating bond David A. Case (Wed Jun 03 2009 - 13:32:57 CDT)
- Re: [AMBER] creating bond Bill Ross (Wed Jun 03 2009 - 13:40:52 CDT)
  - Re: [AMBER] creating bond Jorgen Simonsen (Wed Jun 03 2009 - 14:56:29 CDT)
- Re: [AMBER] creating bond Bill Ross (Wed Jun 03 2009 - 16:40:09 CDT)
  - [AMBER] AMBER 10: sleap diff errors? Catein Catherine (Thu Jun 04 2009 - 00:37:35 CDT)
    - Re: [AMBER] AMBER 10: sleap diff errors? David A. Case (Thu Jun 04 2009 - 14:19:44 CDT)
[AMBER] ptraj image in non-orthorhombic cell Joanna Panecka (Wed Jun 03 2009 - 15:19:52 CDT)
[AMBER] bad atom type in mm_pbsa calculation. How to solve it? Thanks! Haizhen Zhong (Wed Jun 03 2009 - 18:00:34 CDT)
[AMBER] no output when running Antechamber(espgen) xueqin pang (Thu Jun 04 2009 - 01:02:32 CDT)
[AMBER] how to add water for membrane, in Z direction only or xyz xueqin pang (Thu Jun 04 2009 - 03:13:07 CDT)
[AMBER] Binding Energy Vikas Sharma (Thu Jun 04 2009 - 06:25:01 CDT)
[AMBER] Error in MM PBSA Vikas Sharma (Thu Jun 04 2009 - 09:58:43 CDT)
- Re: [AMBER] Error in MM PBSA Ray Luo (Thu Jun 04 2009 - 16:00:51 CDT)
- Re: [AMBER] Error in MM PBSA Vikas Sharma (Sat Jun 06 2009 - 04:03:22 CDT)
  - Re: [AMBER] Error in MM PBSA Ray Luo (Sat Jun 06 2009 - 09:37:43 CDT)
[AMBER] mol2 file to amber pdb file format balaji nagarajan (Thu Jun 04 2009 - 11:32:06 CDT)
- Re: [AMBER] mol2 file to amber pdb file format David A. Case (Thu Jun 04 2009 - 11:55:39 CDT)
[AMBER] rescaling velocities abi ghanem (Thu Jun 04 2009 - 11:39:02 CDT)
- Re: [AMBER] rescaling velocities Carlos Simmerling (Thu Jun 04 2009 - 11:43:20 CDT)
[AMBER] ptraj_hbond_problem balaji nagarajan (Thu Jun 04 2009 - 17:08:24 CDT)
- Re: [AMBER] ptraj_hbond_problem Thomas Cheatham (Fri Jun 05 2009 - 00:28:11 CDT)
[AMBER] Warning: No sp2 improper torsion term for Alan (Fri Jun 05 2009 - 07:26:55 CDT)
- RE: [AMBER] Warning: No sp2 improper torsion term for Ross Walker (Fri Jun 05 2009 - 09:13:53 CDT)
  - Re: [AMBER] Warning: No sp2 improper torsion term for Alan (Mon Jun 08 2009 - 09:54:50 CDT)
[AMBER] parameter for dihedral angle Jorgen Simonsen (Fri Jun 05 2009 - 10:16:56 CDT)
- Re: [AMBER] parameter for dihedral angle David A. Case (Fri Jun 05 2009 - 14:50:03 CDT)
- Re: [AMBER] parameter for dihedral angle raja pandian (Sat Jun 06 2009 - 00:13:52 CDT)
  - Re: [AMBER] parameter for dihedral angle David A. Case (Sat Jun 06 2009 - 07:47:35 CDT)
[AMBER] Proper ISTRNG value ? Marek Maly (Fri Jun 05 2009 - 11:24:58 CDT)
[AMBER] Computational Alanine Scanning using mm_pbsa, any tutorial for amber9 or amber 10 version? Haizhen Zhong (Fri Jun 05 2009 - 18:17:01 CDT)
[AMBER] average torsional energy Francesco Pietra (Sat Jun 06 2009 - 11:57:49 CDT)
- Re: [AMBER] average torsional energy Adrian Roitberg (Sun Jun 07 2009 - 11:09:14 CDT)
  - Re: [AMBER] average torsional energy Carlos Simmerling (Sun Jun 07 2009 - 11:14:17 CDT)
    - Re: [AMBER] average torsional energy Karl Kirschner (Mon Jun 08 2009 - 03:29:05 CDT)
    - Re: [AMBER] average torsional energy Francesco Pietra (Mon Jun 08 2009 - 04:11:52 CDT)
- [AMBER] Fwd: average torsional energy Francesco Pietra (Sun Jun 07 2009 - 11:09:37 CDT)
- [AMBER] How to calculate the distance of CA of all residues in the trajectory Thomas Leonard (Sun Jun 07 2009 - 20:45:54 CDT)
[AMBER] MaxRad ? Marek Maly (Sat Jun 06 2009 - 15:56:44 CDT)
[AMBER] POL3 Hemant Kumar (Sun Jun 07 2009 - 13:27:29 CDT)
[AMBER] vs_vikassharma@yahoo.co.in has sent you a private message Vikas S (Sun Jun 07 2009 - 14:28:00 CDT)
[AMBER] Max filename length in Sander? Paul Mortenson (Mon Jun 08 2009 - 05:59:52 CDT)
- Re: [AMBER] Max filename length in Sander? David A. Case (Mon Jun 08 2009 - 07:28:41 CDT)
  - Re: [AMBER] Max filename length in Sander? Robert Duke (Mon Jun 08 2009 - 12:30:47 CDT)
    - RE: [AMBER] Max filename length in Sander? Paul Mortenson (Tue Jun 09 2009 - 09:47:57 CDT)
    - Re: [AMBER] Max filename length in Sander? Robert Duke (Tue Jun 09 2009 - 10:01:39 CDT)
- Re: [AMBER] Max filename length in Sander? David A. Case (Mon Jun 08 2009 - 07:36:32 CDT)
[AMBER] (no subject) Vishal Maingi (Mon Jun 08 2009 - 06:14:22 CDT)
- Re: [AMBER] (no subject) Karl Kirschner (Mon Jun 08 2009 - 06:38:42 CDT)
- Re: [AMBER] (no subject) FyD (Mon Jun 08 2009 - 12:14:05 CDT)
[AMBER] Lost mail Robert Duke (Mon Jun 08 2009 - 06:58:02 CDT)
[AMBER] problem with creation of prmtop and prmcrd files moitrayee_at_mbu.iisc.ernet.in (Mon Jun 08 2009 - 08:00:18 CDT)
- Re: [AMBER] problem with creation of prmtop and prmcrd files Tom Joseph (Wed Jun 10 2009 - 20:30:19 CDT)
[AMBER] Problem with modified trna[Fwd: problem with creation of prmtop and prmcrd files] moitrayee_at_mbu.iisc.ernet.in (Mon Jun 08 2009 - 09:28:14 CDT)
[AMBER] sander error Beale, John (Mon Jun 08 2009 - 09:43:24 CDT)
- RE: [AMBER] sander error Ross Walker (Mon Jun 08 2009 - 20:41:06 CDT)
  - Re: [AMBER] sander error Robert Duke (Mon Jun 08 2009 - 22:27:52 CDT)
[AMBER] Problem with modified trna[Fwd: problem with creation of prmtop and prmcrd files]] moitrayee_at_mbu.iisc.ernet.in (Mon Jun 08 2009 - 09:30:21 CDT)
[AMBER] Unknown residue: MOL number: 30 type: Terminal/last Workalemhu Berhanu (Mon Jun 08 2009 - 13:30:43 CDT)
- Re: [AMBER] Unknown residue: MOL number: 30 type: Terminal/last David A. Case (Tue Jun 09 2009 - 06:51:42 CDT)
[AMBER] mm_pbsa_statistics-CALC DELTA parameter ? Marek Maly (Mon Jun 08 2009 - 14:16:19 CDT)
[AMBER] Strange contacts with water molecules Jordan MONNET (Mon Jun 08 2009 - 16:39:26 CDT)
- RE: [AMBER] Strange contacts with water molecules Ross Walker (Mon Jun 08 2009 - 22:16:41 CDT)
  - Re: [AMBER] Strange contacts with water molecules Jordan MONNET (Tue Jun 09 2009 - 11:01:53 CDT)
    - Re: [AMBER] Strange contacts with water molecules Jordan MONNET (Wed Jun 17 2009 - 12:00:46 CDT)
[AMBER] Error in MM PBSA (vertex atom mismatch) Vikas Sharma (Tue Jun 09 2009 - 01:33:38 CDT)
[AMBER] ptraj quasiharmonic analysis Neha Gandhi (Tue Jun 09 2009 - 01:38:01 CDT)
- Re: [AMBER] ptraj quasiharmonic analysis Hannes Loeffler (Tue Jun 09 2009 - 02:19:23 CDT)
[AMBER] (no subject) david.lisgarten_at_canterbury.ac.uk (Tue Jun 09 2009 - 05:23:57 CDT)
- Re: [AMBER] (no subject) David A. Case (Tue Jun 09 2009 - 06:47:59 CDT)
  - RE: [AMBER] (no subject) david.lisgarten_at_canterbury.ac.uk (Tue Jun 09 2009 - 08:56:32 CDT)
    - RE: [AMBER] (no subject) david.lisgarten_at_canterbury.ac.uk (Thu Jun 11 2009 - 03:28:56 CDT)
    - Re: [AMBER] (no subject) David A. Case (Thu Jun 11 2009 - 06:54:38 CDT)
[AMBER] SOS - too high binding energy Marek Maly (Tue Jun 09 2009 - 05:49:43 CDT)
- Re: [AMBER] SOS - too high binding energy Marek Maly (Wed Jun 10 2009 - 14:47:58 CDT)
[AMBER] unit of charge in prep files moitrayee_at_mbu.iisc.ernet.in (Tue Jun 09 2009 - 06:35:51 CDT)
- Re: [AMBER] unit of charge in prep files David A. Case (Tue Jun 09 2009 - 08:07:08 CDT)
  - Re: [AMBER] unit of charge in prep files moitrayee_at_mbu.iisc.ernet.in (Tue Jun 09 2009 - 20:18:58 CDT)
[AMBER] Question of about MM-PBSA and mm_pbsa_createinput.pm script Samuel Genheden (Tue Jun 09 2009 - 07:43:19 CDT)
- Re: [AMBER] Question of about MM-PBSA and mm_pbsa_createinput.pm script David A. Case (Tue Jun 09 2009 - 08:20:22 CDT)
[AMBER] Vertex atom mismatch in Amber Vikas Sharma (Tue Jun 09 2009 - 08:41:33 CDT)
[AMBER] DNA as well as protein distorted during MD run in sander Jayalakshmi Sridhar (Tue Jun 09 2009 - 09:30:39 CDT)
- Re: [AMBER] DNA as well as protein distorted during MD run in sander Carlos Simmerling (Tue Jun 09 2009 - 09:38:14 CDT)
- Re: [AMBER] DNA as well as protein distorted during MD run in sander Jayalakshmi Sridhar (Tue Jun 09 2009 - 10:33:51 CDT)
  - Re: [AMBER] DNA as well as protein distorted during MD run in sander Carlos Simmerling (Tue Jun 09 2009 - 10:36:50 CDT)
- Re: [AMBER] DNA as well as protein distorted during MD run in sander Jayalakshmi Sridhar (Tue Jun 09 2009 - 10:44:39 CDT)
  - RE: [AMBER] DNA as well as protein distorted during MD run in sander Jesse Dylan Ziebarth (jziebrth) (Tue Jun 09 2009 - 10:47:34 CDT)
  - Re: [AMBER] DNA as well as protein distorted during MD run in sander Carlos Simmerling (Tue Jun 09 2009 - 10:48:30 CDT)
- Re: [AMBER] DNA as well as protein distorted during MD run in sander Jayalakshmi Sridhar (Tue Jun 09 2009 - 11:02:56 CDT)
[AMBER] Improper dihedrals between residues? Ben Roberts (Tue Jun 09 2009 - 11:11:15 CDT)
- Re: [AMBER] Improper dihedrals between residues? Carlos Simmerling (Tue Jun 09 2009 - 11:28:04 CDT)
  - Re: [AMBER] Improper dihedrals between residues? David A. Case (Tue Jun 09 2009 - 12:14:57 CDT)
    - Re: [AMBER] Improper dihedrals between residues? Carlos Simmerling (Tue Jun 09 2009 - 12:51:40 CDT)
- Re: [AMBER] Improper dihedrals between residues? Bill Ross (Tue Jun 09 2009 - 16:17:03 CDT)
  - [AMBER] radial distribution without normalization CHAMI F. (Wed Jun 10 2009 - 10:48:12 CDT)
    - Re: [AMBER] radial distribution without normalization Thomas Cheatham (Wed Jun 10 2009 - 17:11:40 CDT)
Re: [AMBER] Improper dihedrals between residues? Bill Ross (Tue Jun 09 2009 - 14:04:02 CDT)
- Re: [AMBER] Improper dihedrals between residues? Ben Roberts (Tue Jun 09 2009 - 14:12:07 CDT)
[AMBER] POL3 & SHAKE Hemant Gangwar (Tue Jun 09 2009 - 15:53:27 CDT)
- Re: [AMBER] POL3 & SHAKE David A. Case (Wed Jun 10 2009 - 14:11:40 CDT)
[AMBER] MM PBSA ( Vertex atom mismatch in Amber) Vikas Sharma (Tue Jun 09 2009 - 22:28:22 CDT)
[AMBER] GAFF and solvents.lib error Vishal Maingi (Wed Jun 10 2009 - 05:25:38 CDT)
- Re: [AMBER] GAFF and solvents.lib error David A. Case (Wed Jun 10 2009 - 10:54:05 CDT)
[AMBER] Thermodynamic parameters in mm_PBSA - NAB ? Marek Maly (Wed Jun 10 2009 - 05:33:59 CDT)
- Re: [AMBER] Thermodynamic parameters in mm_PBSA - NAB ? David A. Case (Wed Jun 10 2009 - 11:01:26 CDT)
  - Re: [AMBER] Thermodynamic parameters in mm_PBSA - NAB ? Marek Maly (Wed Jun 10 2009 - 14:47:41 CDT)
[AMBER] partial charges from AM1-BCC and RESP differ a lot xueqin pang (Wed Jun 10 2009 - 07:39:31 CDT)
- Re: [AMBER] partial charges from AM1-BCC and RESP differ a lot FyD (Thu Jun 11 2009 - 13:59:27 CDT)
  - RE:Re: [AMBER] partial charges from AM1-BCC and RESP differ a lot xueqin pang (Tue Jun 16 2009 - 02:57:25 CDT)
    - RE:Re: [AMBER] partial charges from AM1-BCC and RESP differ a lot FyD (Wed Jun 17 2009 - 01:32:11 CDT)
[AMBER] force.f routine Brad Dickson (Wed Jun 10 2009 - 07:56:39 CDT)
- Re: [AMBER] force.f routine David A. Case (Wed Jun 10 2009 - 09:09:47 CDT)
[AMBER] Completed installation of AmberTools, version 1.1 Alan (Wed Jun 10 2009 - 08:13:37 CDT)
- Re: [AMBER] Completed installation of AmberTools, version 1.1 David A. Case (Wed Jun 10 2009 - 09:10:22 CDT)
  - [AMBER] ptraj amber 10 file. Catein Catherine (Wed Jun 10 2009 - 11:02:32 CDT)
[AMBER] Error in AMBER ( Vertex atom mismatch in Amber) Vikas Sharma (Wed Jun 10 2009 - 08:14:28 CDT)
[AMBER] question lev kantorovich (Wed Jun 10 2009 - 09:20:08 CDT)
- RE: [AMBER] question Ross Walker (Wed Jun 10 2009 - 22:19:01 CDT)
[AMBER] compiling amber10 with mac intel, ifort/icc and mpi Alan (Wed Jun 10 2009 - 09:47:00 CDT)
- Re: [AMBER] compiling amber10 with mac intel, ifort/icc and mpi David A. Case (Wed Jun 10 2009 - 10:34:59 CDT)
  - Re: [AMBER] compiling amber10 with mac intel, ifort/icc and mpi Alan (Wed Jun 10 2009 - 11:26:13 CDT)
[AMBER] RNA and polarizable force field Abhishek Singh (Wed Jun 10 2009 - 10:30:29 CDT)
[AMBER] glycopeptide Parametrization guardiani_at_fi.infn.it (Wed Jun 10 2009 - 10:41:14 CDT)
- Re: [AMBER] glycopeptide Parametrization Ahammadunny Pathiaseril (Wed Jun 10 2009 - 15:25:21 CDT)
- Re: [AMBER] glycopeptide Parametrization FyD (Fri Jun 12 2009 - 02:05:51 CDT)
  - Re: [AMBER] glycopeptide Parametrization guardiani_at_fi.infn.it (Fri Jun 12 2009 - 09:06:24 CDT)
[AMBER] GAFF atom type question Cen Gao (Wed Jun 10 2009 - 10:49:00 CDT)
[AMBER] entangle-less building Vishal Maingi (Wed Jun 10 2009 - 12:52:51 CDT)
[AMBER] Generating LeAP file for helix containing non-standard amino acid Brothers, Michael Charles (Wed Jun 10 2009 - 13:26:32 CDT)
- Re: [AMBER] Generating LeAP file for helix containing non-standard amino acid David A. Case (Wed Jun 10 2009 - 14:14:49 CDT)
  - Re: [AMBER] Generating LeAP file for helix containing non-standard amino acid David A. Case (Wed Jun 10 2009 - 14:23:36 CDT)
    - RE: [AMBER] Generating LeAP file for helix containing non-standard amino acid Brothers, Michael Charles (Wed Jun 10 2009 - 14:40:21 CDT)
- Re: [AMBER] Generating LeAP file for helix containing non-standard amino acid FyD (Thu Jun 11 2009 - 01:48:27 CDT)
  - RE: [AMBER] Generating LeAP file for helix containing non-standard amino acid Brothers, Michael Charles (Thu Jun 18 2009 - 12:38:53 CDT)
[AMBER] input coordinates for vdW transition step in Amber 10 TI Jodi Hadden (Wed Jun 10 2009 - 15:27:16 CDT)
- Re: [AMBER] input coordinates for vdW transition step in Amber 10 TI Tom Joseph (Wed Jun 10 2009 - 20:02:51 CDT)
- Re: [AMBER] input coordinates for vdW transition step in Amber 10 TI Ye MEI (Thu Jun 11 2009 - 03:22:34 CDT)
- Re: [AMBER] input coordinates for vdW transition step in Amber 10 TI steinbrt_at_rci.rutgers.edu (Thu Jun 11 2009 - 05:42:51 CDT)
Re: [AMBER] entangle-less building Bill Ross (Wed Jun 10 2009 - 17:38:31 CDT)
- [AMBER] Constant pH simulation Rukman Hertadi (Wed Jun 10 2009 - 19:56:59 CDT)
  - Re: [AMBER] Constant pH simulation Tom Joseph (Wed Jun 10 2009 - 20:08:36 CDT)
[AMBER] Vertex atom mismatch in Amber Vikas Sharma (Wed Jun 10 2009 - 22:29:57 CDT)
[AMBER] zinc coordination of benzimidazole Aust, Susanne (Thu Jun 11 2009 - 02:09:59 CDT)
- Re: [AMBER] zinc coordination of benzimidazole Urszula Uciechowska (Thu Jun 11 2009 - 03:49:45 CDT)
  - [AMBER] ptraj "image" "center" commands Catein Catherine (Thu Jun 11 2009 - 04:13:38 CDT)
    - RE: [AMBER] ptraj "image" "center" commands Ross Walker (Thu Jun 11 2009 - 10:30:08 CDT)
[AMBER] NOE Beale, John (Thu Jun 11 2009 - 07:30:36 CDT)
- Re: [AMBER] NOE David A. Case (Thu Jun 11 2009 - 12:29:06 CDT)
[AMBER] GAFF atom type question Cen Gao (Thu Jun 11 2009 - 08:36:52 CDT)
- RE: [AMBER] GAFF atom type question Ross Walker (Thu Jun 11 2009 - 10:43:50 CDT)
  - Re: [AMBER] GAFF atom type question Cen Gao (Thu Jun 11 2009 - 19:31:25 CDT)
  - Re: [AMBER] GAFF atom type question Cen Gao (Sun Jun 14 2009 - 23:12:19 CDT)
- [AMBER] cpin error Rukman Hertadi (Fri Jul 24 2009 - 02:18:52 CDT)
  - Re: [AMBER] cpin error case (Fri Jul 24 2009 - 14:41:00 CDT)
    - RE: [AMBER] cpin error Rukman Hertadi (Tue Jul 28 2009 - 00:22:18 CDT)
    - Re: [AMBER] cpin error case (Tue Sep 01 2009 - 07:23:04 CDT)
[AMBER] Copper semiempirical parameters Jacopo Sgrignani (Thu Jun 11 2009 - 08:49:50 CDT)
- RE: [AMBER] Copper semiempirical parameters Ross Walker (Thu Jun 11 2009 - 11:09:14 CDT)
[AMBER] PRINCIPAL QUESTION Marek Maly (Thu Jun 11 2009 - 10:41:42 CDT)
[AMBER] setBox truncated octahedron Myunggi Yi (Thu Jun 11 2009 - 12:27:26 CDT)
AW: [AMBER] zinc coordination of benzimidazole Aust, Susanne (Fri Jun 12 2009 - 01:13:19 CDT)
[AMBER] MM PBSA ERROR Vikas Sharma (Fri Jun 12 2009 - 09:04:25 CDT)
[AMBER] Residues KIRTANA S (Fri Jun 12 2009 - 09:10:39 CDT)
- Re: [AMBER] Residues FyD (Fri Jun 12 2009 - 09:24:35 CDT)
  - Re: [AMBER] Residues KIRTANA S (Fri Jun 12 2009 - 10:07:50 CDT)
- Re: [AMBER] Residues Bill Ross (Fri Jun 12 2009 - 14:49:09 CDT)
- [AMBER] Re: Residues KIRTANA S (Fri Jun 12 2009 - 20:15:20 CDT)
- Re: [AMBER] Residues FyD (Mon Jun 15 2009 - 01:51:56 CDT)
- Re: [AMBER] Residues KIRTANA S (Thu Jun 18 2009 - 14:57:11 CDT)
  - Re: [AMBER] Residues FyD (Thu Jun 18 2009 - 15:24:16 CDT)
- Re: [AMBER] Residues Bill Ross (Thu Jun 18 2009 - 16:13:53 CDT)
  - Re: [AMBER] Residues Roman Osman (Thu Jun 18 2009 - 16:58:53 CDT)
[AMBER] help KIRTANA S (Fri Jun 12 2009 - 08:42:04 CDT)
- RE: [AMBER] help Ross Walker (Fri Jun 12 2009 - 11:02:06 CDT)
[AMBER] dipole printing Hemant Kumar (Fri Jun 12 2009 - 10:58:29 CDT)
- RE: [AMBER] dipole printing Ross Walker (Fri Jun 12 2009 - 11:13:30 CDT)
  - RE: [AMBER] dipole printing Hemant Kumar (Fri Jun 12 2009 - 14:03:17 CDT)
[AMBER] AMBER ERROR Vikas Sharma (Sat Jun 13 2009 - 02:16:52 CDT)
[AMBER] Re: [Contact q4md] qurey reagarding RED Server FyD (Sat Jun 13 2009 - 03:08:26 CDT)
[AMBER] too high in binding energy (MM-PBSA) Maryam Hamzehee (Sat Jun 13 2009 - 04:53:43 CDT)
- å›žå¤ï¼š [AMBER] too high in binding energy (MM-PBSA) å»–é’åŽ (Sat Jun 13 2009 - 07:44:31 CDT)
  - Re: å›žå¤ï¼š [AMBER] too high in binding energy (MM-PBSA) Maryam Hamzehee (Sat Jun 13 2009 - 08:56:16 CDT)
[AMBER] PLEASE HELP - PDB Modification s_bill36_at_yahoo.co.uk (Sun Jun 14 2009 - 12:29:31 CDT)
- Re: [AMBER] PLEASE HELP - PDB Modification Tom Joseph (Sun Jun 14 2009 - 18:36:16 CDT)
[AMBER] parallel error å»–é’åŽ (Mon Jun 15 2009 - 02:31:27 CDT)
- Re: [AMBER] parallel error Tom Joseph (Mon Jun 15 2009 - 06:54:19 CDT)
  - å›žå¤ï¼š [AMBER] parallel error å»–é’åŽ (Mon Jun 15 2009 - 07:08:27 CDT)
[AMBER] covalent interaction å»–é’åŽ (Mon Jun 15 2009 - 03:06:52 CDT)
[AMBER] total charge for NPRO in ff03ua Edyta Malolepsza (Mon Jun 15 2009 - 05:09:35 CDT)
- RE: [AMBER] total charge for NPRO in ff03ua Jun Wang (Mon Jun 15 2009 - 18:35:39 CDT)
  - Re: [AMBER] total charge for NPRO in ff03ua Edyta Malolepsza (Tue Jun 16 2009 - 04:42:55 CDT)
[AMBER] to unsubscribe email Urszula Uciechowska (Mon Jun 15 2009 - 07:59:46 CDT)
- RE: [AMBER] to unsubscribe email Ross Walker (Mon Jun 15 2009 - 11:59:06 CDT)
- [AMBER] to unsubscribe email backy (Wed Jun 17 2009 - 02:13:02 CDT)
  - RE: [AMBER] to unsubscribe email Ross Walker (Wed Jun 17 2009 - 03:09:39 CDT)
    - Re: [AMBER] to unsubscribe email backy (Wed Jun 17 2009 - 03:22:19 CDT)
[AMBER] Antechamber am1bcc questions gilbert_at_bluemarble.net (Mon Jun 15 2009 - 08:04:19 CDT)
[AMBER] to check basepair in ptraj balaji nagarajan (Mon Jun 15 2009 - 09:23:28 CDT)
[AMBER] Histidine, which form? s_bill36_at_yahoo.co.uk (Mon Jun 15 2009 - 09:54:05 CDT)
- Re: [AMBER] Histidine, which form? Carlos Simmerling (Mon Jun 15 2009 - 09:57:40 CDT)
- RE: [AMBER] Histidine, which form? Ross Walker (Mon Jun 15 2009 - 10:06:49 CDT)
- Re: [AMBER] Histidine, which form? s. Bill (Mon Jun 15 2009 - 11:28:27 CDT)
  - RE: [AMBER] Histidine, which form? Ross Walker (Mon Jun 15 2009 - 11:39:04 CDT)
    - Re: [AMBER] Histidine, which form? M. L. Dodson (Mon Jun 15 2009 - 11:45:25 CDT)
[AMBER] pKa data base.... s. Bill (Mon Jun 15 2009 - 11:01:14 CDT)
[AMBER] Need help with nab code to access the m_prm struct in a molecule M. L. Dodson (Mon Jun 15 2009 - 14:49:02 CDT)
[AMBER] Re: connect KIRTANA S (Mon Jun 15 2009 - 15:18:54 CDT)
- RE: [AMBER] Re: connect Ross Walker (Mon Jun 15 2009 - 20:43:46 CDT)
- [AMBER] Distance-covariance and PCA questions... Cihan Aydin (Mon Jun 15 2009 - 23:18:58 CDT)
  - Re: [AMBER] Distance-covariance and PCA questions... Hannes Loeffler (Wed Jun 17 2009 - 02:41:42 CDT)
Re: [AMBER] Re: connect Bill Ross (Mon Jun 15 2009 - 15:39:32 CDT)
[AMBER] problem in pressure equillibration wong105_at_llnl.gov (Tue Jun 16 2009 - 01:18:22 CDT)
- Re: [AMBER] problem in pressure equillibration David A. Case (Tue Jun 16 2009 - 06:56:34 CDT)
[AMBER] Fix the local structure as a rigid body Yunjie Zhao (Tue Jun 16 2009 - 08:11:43 CDT)
- Re: [AMBER] Fix the local structure as a rigid body Carlos Simmerling (Tue Jun 16 2009 - 08:15:12 CDT)
  - Re: [AMBER] Fix the local structure as a rigid body Yunjie Zhao (Tue Jun 16 2009 - 08:57:10 CDT)
    - Re: [AMBER] Fix the local structure as a rigid body Carlos Simmerling (Tue Jun 16 2009 - 09:13:45 CDT)
    - Re: [AMBER] Fix the local structure as a rigid body David A. Case (Tue Jun 16 2009 - 10:41:04 CDT)
[AMBER] Sander imin=5 option Paul Mortenson (Tue Jun 16 2009 - 09:46:37 CDT)
- Re: [AMBER] Sander imin=5 option Carlos Simmerling (Tue Jun 16 2009 - 09:50:43 CDT)
  - RE: [AMBER] Sander imin=5 option Paul Mortenson (Tue Jun 16 2009 - 10:09:54 CDT)
[AMBER] MM decomp energy - zero values for Eele, Evdw Thomas Lake (Tue Jun 16 2009 - 10:36:50 CDT)
[AMBER] connecting residues KIRTANA S (Tue Jun 16 2009 - 10:59:37 CDT)
Re: [AMBER] Distance-covariance and PCA questions... Bill Ross (Tue Jun 16 2009 - 11:18:40 CDT)
Re: [AMBER] connecting residues Bill Ross (Tue Jun 16 2009 - 11:37:33 CDT)
- Re: [AMBER] connecting residues Bill Ross (Tue Jun 16 2009 - 11:39:02 CDT)
[AMBER] Seg-fault when creating residue Valla Fatemi (Tue Jun 16 2009 - 20:28:43 CDT)
- [AMBER] Re: Seg-fault when creating residue Valla Fatemi (Wed Jun 17 2009 - 12:41:47 CDT)
[AMBER] improper torsion problem Youn Kyeung Lee (Tue Jun 16 2009 - 21:36:14 CDT)
[AMBER] GLYCAM: warnings by writing topology Sergey Samsonov (Wed Jun 17 2009 - 01:38:56 CDT)
- Re: [AMBER] GLYCAM: warnings by writing topology FyD (Wed Jun 17 2009 - 02:30:26 CDT)
  - Re: [AMBER] GLYCAM: warnings by writing topology Sergey Samsonov (Wed Jun 17 2009 - 02:50:46 CDT)
  - Re: [AMBER] GLYCAM: warnings by writing topology Sergey Samsonov (Wed Jun 17 2009 - 03:18:33 CDT)
- Re: [AMBER] GLYCAM: warnings by writing topology Bill Ross (Wed Jun 17 2009 - 03:01:28 CDT)
  - Re: [AMBER] GLYCAM: warnings by writing topology Sergey Samsonov (Wed Jun 17 2009 - 03:10:33 CDT)
- Re: [AMBER] GLYCAM: warnings by writing topology Bill Ross (Wed Jun 17 2009 - 12:32:43 CDT)
  - Re: [AMBER] GLYCAM: warnings by writing topology Sergey Samsonov (Thu Jun 18 2009 - 07:49:31 CDT)
[AMBER] How to calculate SASA in vmd Mannan (Wed Jun 17 2009 - 01:40:05 CDT)
Re: [AMBER] improper torsion problem Bill Ross (Wed Jun 17 2009 - 02:47:12 CDT)
Re: [AMBER] Seg-fault when creating residue Bill Ross (Wed Jun 17 2009 - 02:51:02 CDT)
[AMBER] vlimit in TI with soft core potential Ye MEI (Wed Jun 17 2009 - 03:20:31 CDT)
- Re: [AMBER] vlimit in TI with soft core potential steinbrt_at_rci.rutgers.edu (Wed Jun 17 2009 - 03:47:38 CDT)
  - Re: [AMBER] vlimit in TI with soft core potential Ye MEI (Wed Jun 17 2009 - 04:13:40 CDT)
[AMBER] Antechamber: stuck at bondtype Jack Shultz (Wed Jun 17 2009 - 07:50:11 CDT)
- Re: [AMBER] Antechamber: stuck at bondtype David A. Case (Wed Jun 17 2009 - 08:28:15 CDT)
- Re: [AMBER] Antechamber: stuck at bondtype Ye MEI (Wed Jun 17 2009 - 08:48:18 CDT)
[AMBER] bond length energy Thomas Lake (Wed Jun 17 2009 - 09:04:55 CDT)
- Re: [AMBER] bond length energy Mark Williamson (Wed Jun 17 2009 - 12:29:09 CDT)
- Re: [AMBER] bond length energy Karl Kirschner (Fri Jun 19 2009 - 04:57:04 CDT)
[AMBER] Specifying improper dihedrals Ben Roberts (Wed Jun 17 2009 - 10:24:14 CDT)
- Re: [AMBER] Specifying improper dihedrals Mark Williamson (Wed Jun 17 2009 - 12:12:08 CDT)
  - Re: [AMBER] Specifying improper dihedrals David A. Case (Wed Jun 17 2009 - 12:56:20 CDT)
    - Re: [AMBER] Specifying improper dihedrals Ben Roberts (Wed Jun 17 2009 - 14:17:12 CDT)
- Re: [AMBER] Specifying improper dihedrals Bill Ross (Wed Jun 17 2009 - 12:56:26 CDT)
  - Re: [AMBER] Specifying improper dihedrals Ben Roberts (Wed Jun 17 2009 - 14:18:41 CDT)
- Re: [AMBER] Specifying improper dihedrals Bill Ross (Wed Jun 17 2009 - 14:25:55 CDT)
[AMBER] Coarse grained MD in AMBER ? Siddharth Rastogi (Wed Jun 17 2009 - 13:50:13 CDT)
- Re: [AMBER] Coarse grained MD in AMBER ? Lili Peng (Wed Jun 17 2009 - 13:57:58 CDT)
[AMBER] where to I get the parameters for Mg divalent ion Mannan (Wed Jun 17 2009 - 23:11:19 CDT)
- Re: [AMBER] where to I get the parameters for Mg divalent ion Tom Joseph (Thu Jun 18 2009 - 22:53:01 CDT)
[AMBER] force units Brad Dickson (Thu Jun 18 2009 - 02:14:31 CDT)
- [AMBER] Re: force units Brad Dickson (Thu Jun 18 2009 - 04:31:16 CDT)
  - Re: [AMBER] Re: force units David A. Case (Thu Jun 18 2009 - 06:32:18 CDT)
    - [AMBER] ptraj correlation Catein Catherine (Thu Jun 18 2009 - 08:47:01 CDT)
    - RE: [AMBER] Re: force units Catein Catherine (Thu Jun 18 2009 - 09:01:40 CDT)
  - [AMBER] Re: force units Brad Dickson (Fri Jun 19 2009 - 08:22:40 CDT)
[AMBER] Improper dihedrals from .off and .lib files Johan Sund (Thu Jun 18 2009 - 05:15:37 CDT)
- Re: [AMBER] Improper dihedrals from .off and .lib files David A. Case (Thu Jun 18 2009 - 06:28:40 CDT)
[AMBER] guntheyp_at_aston.ac.uk (Thu Jun 18 2009 - 06:48:21 CDT)
- Re: [AMBER] Raja Pandian (Thu Jun 18 2009 - 07:35:10 CDT)
[AMBER] how to create prmtop and inpcrd files for covalent neutral phenylalanine Madhurima Jana (Thu Jun 18 2009 - 07:39:03 CDT)
[AMBER] Sulfates parameterization for GAGs in GLYCAM_06 Sergey Samsonov (Thu Jun 18 2009 - 08:07:17 CDT)
[AMBER] Dyndom Chunliyan (Thu Jun 18 2009 - 10:12:44 CDT)
[AMBER] Fix Residue continued... Vishal Maingi (Thu Jun 18 2009 - 13:48:03 CDT)
- Re: [AMBER] Fix Residue continued... Carlos Simmerling (Thu Jun 18 2009 - 13:56:54 CDT)
[AMBER] residue KIRTANA S (Thu Jun 18 2009 - 14:59:50 CDT)
[AMBER] Re: R.E.D. error message FyD (Thu Jun 18 2009 - 15:13:41 CDT)
[AMBER] Postdoc position in biomolecular simulation Ivaylo, Ivanov (Thu Jun 18 2009 - 18:26:05 CDT)
[AMBER] From DLG to Antechamber Jack Shultz (Thu Jun 18 2009 - 19:04:15 CDT)
- Re: [AMBER] From DLG to Antechamber FyD (Fri Jun 19 2009 - 04:26:46 CDT)
  - Re: [AMBER] From DLG to Antechamber Jack Shultz (Fri Jun 19 2009 - 07:27:20 CDT)
- Re: [AMBER] From DLG to Antechamber gilbert_at_bluemarble.net (Fri Jun 19 2009 - 07:57:04 CDT)
  - Re: [AMBER] From DLG to Antechamber Jack Shultz (Fri Jun 19 2009 - 08:09:06 CDT)
- Re: [AMBER] From DLG to Antechamber FyD (Fri Jun 19 2009 - 10:54:05 CDT)
[AMBER] Force field parameter for Unionized Phenylalanine HOOC-CH(NH2)-CH2-C6H5 Madhurima Jana (Fri Jun 19 2009 - 01:40:43 CDT)
- Re: [AMBER] Force field parameter for Unionized Phenylalanine HOOC-CH(NH2)-CH2-C6H5 FyD (Fri Jun 19 2009 - 03:47:39 CDT)
[AMBER] 2 restraints with different force constants Aust, Susanne (Fri Jun 19 2009 - 02:14:50 CDT)
- Re: [AMBER] 2 restraints with different force constants David A. Case (Fri Jun 19 2009 - 06:41:01 CDT)
AW: [AMBER] 2 restraints with different force constants Aust, Susanne (Fri Jun 19 2009 - 06:51:21 CDT)
- Re: [AMBER] 2 restraints with different force constants David A. Case (Fri Jun 19 2009 - 07:06:18 CDT)
[AMBER] methyl group at the N-terminal Francesca Poletti (Fri Jun 19 2009 - 07:03:56 CDT)
- Re: [AMBER] methyl group at the N-terminal FyD (Fri Jun 19 2009 - 07:12:36 CDT)
AW: [AMBER] 2 restraints with different force constants Aust, Susanne (Fri Jun 19 2009 - 07:39:34 CDT)
[AMBER] Re: residue KIRTANA S (Fri Jun 19 2009 - 10:03:31 CDT)
[AMBER] RED Geometry Calculation Error Brothers, Michael Charles (Fri Jun 19 2009 - 13:52:37 CDT)
- Re: [AMBER] RED Geometry Calculation Error FyD (Fri Jun 19 2009 - 14:19:00 CDT)
  - RE: [AMBER] RED Geometry Calculation Error Brothers, Michael Charles (Fri Jun 19 2009 - 16:10:12 CDT)
[AMBER] atom type no recognize - xleap version 10 but fine in v 9 Peter Gannett (Fri Jun 19 2009 - 14:40:47 CDT)
- Re: [AMBER] atom type no recognize - xleap version 10 but fine in v 9 case (Sat Jun 20 2009 - 13:31:40 CDT)
[AMBER] PMEMD compilation manoj singh (Fri Jun 19 2009 - 17:49:31 CDT)
- RE: [AMBER] PMEMD compilation Ross Walker (Sat Jun 20 2009 - 12:36:14 CDT)
  - Re: [AMBER] PMEMD compilation manoj singh (Sat Jun 20 2009 - 23:05:44 CDT)
[AMBER] Hard limit in Amber10? Yang, Ping (Fri Jun 19 2009 - 19:21:14 CDT)
- RE: [AMBER] Hard limit in Amber10? Ross Walker (Sat Jun 20 2009 - 12:40:46 CDT)
  - RE: [AMBER] Hard limit in Amber10? Yang, Ping (Sat Jun 20 2009 - 18:44:11 CDT)
    - RE: [AMBER] Hard limit in Amber10? Yang, Ping (Mon Jun 22 2009 - 20:52:39 CDT)
    - RE: [AMBER] Hard limit in Amber10? Ross Walker (Wed Jun 24 2009 - 11:02:17 CDT)
[AMBER] Amber10 Parallel Installation Hopkins, Robert (Sat Jun 20 2009 - 14:50:16 CDT)
- Re: [AMBER] Amber10 Parallel Installation case (Sat Jun 20 2009 - 17:04:14 CDT)
R: [AMBER] Amber10 Parallel Installation sgrignani_at_cerm.unifi.it (Sat Jun 20 2009 - 15:14:38 CDT)
[AMBER] Your private message from Vikas is about to expire Vikas S (Sun Jun 21 2009 - 01:40:41 CDT)
[AMBER] Reference Correction Mahmoud A. A. Ibrahim (Sun Jun 21 2009 - 15:11:34 CDT)
[AMBER] reclaiming space from amber10 installation Alan (Sun Jun 21 2009 - 17:04:53 CDT)
- [AMBER] correlation motion at production simulation period still changing. Is it normal? Catein Catherine (Mon Jun 22 2009 - 04:26:40 CDT)
- RE: [AMBER] reclaiming space from amber10 installation Ross Walker (Mon Jun 22 2009 - 20:26:36 CDT)
[AMBER] parameters Fe4S4 cluster KIRTANA S (Sun Jun 21 2009 - 21:30:08 CDT)
[AMBER] Atom Type List Javier Klett (Mon Jun 22 2009 - 04:54:43 CDT)
- Re: [AMBER] Atom Type List case (Mon Jun 22 2009 - 06:38:24 CDT)
  - Re: [Barracuda SPAM] Re: [AMBER] Atom Type List Javier Klett (Mon Jun 22 2009 - 11:34:43 CDT)
    - Re: [Barracuda SPAM] Re: [AMBER] Atom Type List Bill Ross (Mon Jun 22 2009 - 11:43:39 CDT)
[AMBER] About the Amber tutorial Aurum Bai (Mon Jun 22 2009 - 05:03:49 CDT)
[AMBER] About the "FATAL: Atom err!" Aurum Bai (Mon Jun 22 2009 - 05:12:23 CDT)
[AMBER] About the "FATAL: Atom err"! Aurum Bai (Mon Jun 22 2009 - 05:14:20 CDT)
- Re: [AMBER] About the "FATAL: Atom err"! case (Mon Jun 22 2009 - 06:47:59 CDT)
[AMBER] Error on equilibriation of Amber10 Masakazu SEKIJIMA (Mon Jun 22 2009 - 05:59:55 CDT)
- Re: [AMBER] Problems using nmode in NAB Andreas Svrcek-Seiler (Wed Jun 24 2009 - 03:52:30 CDT)
  - Re: [AMBER] Problems using nmode in NAB E.M. (Wed Jun 24 2009 - 04:09:44 CDT)
  - Re: [AMBER] Problems using nmode in NAB E.M. (Wed Jun 24 2009 - 23:15:38 CDT)
    - Re: [AMBER] Problems using nmode in NAB Andreas Svrcek-Seiler (Thu Jun 25 2009 - 08:03:15 CDT)
- [AMBER] Re: Error on equilibriation of Amber10 Masakazu SEKIJIMA (Thu Jun 25 2009 - 05:45:31 CDT)
  - Re: [AMBER] Re: Error on equilibriation of Amber10 case (Thu Jun 25 2009 - 07:07:20 CDT)
    - Re: [AMBER] Re: Error on equilibriation of Amber10 Masakazu SEKIJIMA (Thu Jun 25 2009 - 12:41:39 CDT)
    - Re: [AMBER] Re: Error on equilibriation of Amber10 case (Fri Jun 26 2009 - 07:17:42 CDT)
[AMBER] max atoms for antechamber Alan (Mon Jun 22 2009 - 07:37:39 CDT)
- Re: [AMBER] max atoms for antechamber case (Mon Jun 22 2009 - 07:48:43 CDT)
  - Re: [AMBER] max atoms for antechamber Alan (Mon Jun 22 2009 - 08:00:48 CDT)
[AMBER] making leap to recognize 5' phosphate Bala subramanian (Mon Jun 22 2009 - 08:45:43 CDT)
- Re: [AMBER] making leap to recognize 5' phosphate FyD (Tue Jun 23 2009 - 02:45:31 CDT)
  - Re: [AMBER] making leap to recognize 5' phosphate Bala subramanian (Tue Jun 23 2009 - 03:49:05 CDT)
    - Re: [AMBER] making leap to recognize 5' phosphate FyD (Tue Jun 23 2009 - 04:48:34 CDT)
- Re: [AMBER] making leap to recognize 5' phosphate FyD (Wed Jun 24 2009 - 01:02:42 CDT)
[AMBER] Re: Regd: Fe4S4 case (Mon Jun 22 2009 - 13:39:57 CDT)
RE: [Subject Filtered] Re: [AMBER] Amber10 Parallel Installation 8% Hopkins, Robert (Mon Jun 22 2009 - 14:54:17 CDT)
[AMBER] bad atom type: MN Edward M (Mon Jun 22 2009 - 18:10:54 CDT)
[AMBER] bad atom type: MN Edward M (Mon Jun 22 2009 - 18:12:09 CDT)
[AMBER] bad atom type: MN Edward M (Mon Jun 22 2009 - 18:12:09 CDT)
[AMBER] AMBER question: bad atom type: MN Edward M (Mon Jun 22 2009 - 22:05:51 CDT)
[AMBER] REMD Shaikh Abdul R S Ramaju (Tue Jun 23 2009 - 00:32:34 CDT)
- Re: [AMBER] REMD Carlos Simmerling (Tue Jun 23 2009 - 05:07:39 CDT)
[AMBER] guessing the charge of a small molecule Alan (Tue Jun 23 2009 - 03:06:51 CDT)
[AMBER] Compiling amber 9 with openMPI Myunggi Yi (Tue Jun 23 2009 - 08:31:58 CDT)
- Re: [AMBER] Compiling amber 9 with openMPI case (Tue Jun 23 2009 - 09:13:18 CDT)
  - Re: [AMBER] Compiling amber 9 with openMPI Myunggi Yi (Tue Jun 23 2009 - 13:11:46 CDT)
[AMBER] net charge Vishal Maingi (Tue Jun 23 2009 - 09:19:51 CDT)
- Re: [AMBER] net charge case (Tue Jun 23 2009 - 09:34:07 CDT)
[AMBER] SANDER BOMB in subroutine nonbond_list Siddharth Rastogi (Tue Jun 23 2009 - 11:39:58 CDT)
Re: [AMBER] SANDER BOMB in subroutine nonbond_list Bill Ross (Tue Jun 23 2009 - 11:54:30 CDT)
[AMBER] re: net charge Vishal Maingi (Tue Jun 23 2009 - 13:56:52 CDT)
- Re: [AMBER] re: net charge case (Tue Jun 23 2009 - 14:22:28 CDT)
  - Re: [AMBER] re: net charge Junmei Wang (Tue Jun 23 2009 - 15:41:24 CDT)
[AMBER] "loadoff tRNA.lib" in Leap Ju Zhang (Tue Jun 23 2009 - 15:55:25 CDT)
[AMBER] 2-step vs 3-step TI, and softcores question Jodi Hadden (Tue Jun 23 2009 - 17:00:02 CDT)
- Re: [AMBER] 2-step vs 3-step TI, and softcores question steinbrt_at_rci.rutgers.edu (Tue Jun 23 2009 - 17:27:46 CDT)
[AMBER] How to build amide bond etween two protein chains journal.update (Tue Jun 23 2009 - 23:36:07 CDT)
- Re: [AMBER] How to build amide bond etween two protein chains FyD (Wed Jun 24 2009 - 01:18:25 CDT)
[AMBER] error in tleap of AMBER 10 kureeckal ramesh (Wed Jun 24 2009 - 00:03:55 CDT)
- Re: [AMBER] error in tleap of AMBER 10 case (Thu Jun 25 2009 - 06:54:47 CDT)
[AMBER] Problems using nmode in NAB E.M. (Wed Jun 24 2009 - 01:05:50 CDT)
[AMBER] calculating the hydrogen bonding energy between the two molecule bharat lakhani (Wed Jun 24 2009 - 04:19:01 CDT)
[AMBER] Trying to patch amber 9 Jack Shultz (Wed Jun 24 2009 - 08:24:40 CDT)
- Re: [AMBER] Trying to patch amber 9 case (Wed Jun 24 2009 - 09:58:48 CDT)
  - Re: [AMBER] Trying to patch amber 9 Jack Shultz (Wed Jun 24 2009 - 10:18:23 CDT)
    - Re: [AMBER] Trying to patch amber 9 Jack Shultz (Wed Jun 24 2009 - 10:25:41 CDT)
[AMBER] Half charge reported during NN ? Marek Maly (Wed Jun 24 2009 - 11:33:54 CDT)
- Re: [AMBER] Half charge reported during NN ? case (Wed Jun 24 2009 - 12:31:45 CDT)
  - Re: [AMBER] Half charge reported during NN ? Marek Maly (Wed Jun 24 2009 - 12:43:26 CDT)
[AMBER] problem with parametrization janzso_at_brc.hu (Wed Jun 24 2009 - 13:24:45 CDT)
- RE: [AMBER] problem with parametrization Brothers, Michael Charles (Wed Jun 24 2009 - 13:34:16 CDT)
- Re: [AMBER] problem with parametrization FyD (Thu Jun 25 2009 - 00:15:23 CDT)
  - Re: [AMBER] problem with parametrization janzso_at_brc.hu (Thu Jun 25 2009 - 04:49:50 CDT)
- Re: [AMBER] problem with parametrization FyD (Thu Jun 25 2009 - 05:04:27 CDT)
  - Re: [AMBER] problem with parametrization janzso_at_brc.hu (Thu Jun 25 2009 - 06:40:35 CDT)
[AMBER] Amber tools 1.2 , Bug report (PTRAJ: dumpq with strip) Myunggi Yi (Wed Jun 24 2009 - 13:57:25 CDT)
[AMBER] NAB memory increase E.M. (Wed Jun 24 2009 - 15:12:09 CDT)
- Re: [AMBER] NAB memory increase case (Thu Jun 25 2009 - 06:33:03 CDT)
- Re: [AMBER] NAB memory increase Bill Ross (Thu Jun 25 2009 - 11:34:58 CDT)
[AMBER] setting atomic radii for GB version 7 Workalemhu Berhanu (Wed Jun 24 2009 - 22:12:55 CDT)
- Re: [AMBER] setting atomic radii for GB version 7 case (Thu Jun 25 2009 - 07:20:36 CDT)
[AMBER] atomtypes in gaff Aust, Susanne (Thu Jun 25 2009 - 01:49:48 CDT)
- Re: [AMBER] atomtypes in gaff FyD (Thu Jun 25 2009 - 03:55:03 CDT)
[AMBER] Re: question about ff FyD (Thu Jun 25 2009 - 04:12:40 CDT)
[AMBER] ADD SALT Rilei Yu (Thu Jun 25 2009 - 04:22:20 CDT)
- Re: [AMBER] ADD SALT Simon Becker (Thu Jun 25 2009 - 04:57:37 CDT)
AW: [AMBER] atomtypes in gaff Aust, Susanne (Thu Jun 25 2009 - 04:24:07 CDT)
- Re: AW: [AMBER] atomtypes in gaff FyD (Thu Jun 25 2009 - 05:32:33 CDT)
AW: AW: [AMBER] atomtypes in gaff Aust, Susanne (Thu Jun 25 2009 - 06:27:19 CDT)
- Re: AW: AW: [AMBER] atomtypes in gaff FyD (Thu Jun 25 2009 - 06:36:20 CDT)
- Re: [AMBER] atomtypes in gaff FyD (Thu Jun 25 2009 - 06:45:16 CDT)
[AMBER] PCA for CA of specific resiudes Patrick Gedeon (Thu Jun 25 2009 - 06:43:20 CDT)
- Re: [AMBER] PCA for CA of specific resiudes case (Thu Jun 25 2009 - 07:27:01 CDT)
AW: AW: AW: [AMBER] atomtypes in gaff Aust, Susanne (Thu Jun 25 2009 - 06:44:58 CDT)
AW: [AMBER] atomtypes in gaff Aust, Susanne (Thu Jun 25 2009 - 07:05:10 CDT)
- Re: AW: [AMBER] atomtypes in gaff FyD (Fri Jun 26 2009 - 01:56:35 CDT)
[AMBER] Error when installing amber11 on OpenSuse steinbrt_at_rci.rutgers.edu (Thu Jun 25 2009 - 07:19:59 CDT)
[AMBER] ADD SALT additional question Simon Becker (Thu Jun 25 2009 - 07:34:36 CDT)
- Re: [AMBER] ADD SALT additional question Vlad Cojocaru (Thu Jun 25 2009 - 09:51:54 CDT)
- Re: [AMBER] ADD SALT additional question Vlad Cojocaru (Thu Jun 25 2009 - 09:55:15 CDT)
[AMBER] ptraj clustering with sieve- unexpected Bus Error Rachel Rice (Thu Jun 25 2009 - 10:24:25 CDT)
- Re: [AMBER] ptraj clustering with sieve- unexpected Bus Error David Watson (Thu Jun 25 2009 - 13:53:16 CDT)
  - Re: [AMBER] ptraj clustering with sieve- unexpected Bus Error Rachel Rice (Thu Jun 25 2009 - 19:54:31 CDT)
Re: AW: [AMBER] atomtypes in gaff Bill Ross (Thu Jun 25 2009 - 11:42:01 CDT)
[AMBER] Compiling and running NAB programs in parallel using MPI Kaushik Raha (Thu Jun 25 2009 - 16:36:35 CDT)
- Re: [AMBER] Compiling and running NAB programs in parallel using MPI case (Fri Jun 26 2009 - 08:19:04 CDT)
  - Re: [AMBER] Compiling and running NAB programs in parallel using MPI Kaushik Raha (Fri Jun 26 2009 - 10:12:11 CDT)
[AMBER] Thanks Simon and Vlad! Rilei Yu (Thu Jun 25 2009 - 18:32:35 CDT)
[AMBER] error in tleap of AMBER 10 kureeckal ramesh (Fri Jun 26 2009 - 02:10:56 CDT)
- Re: [AMBER] error in tleap of AMBER 10 case (Fri Jun 26 2009 - 07:09:58 CDT)
[AMBER] Box Center Jagan Mohan (Fri Jun 26 2009 - 03:02:05 CDT)
[AMBER] installation of RESP programm subarna thakur (Fri Jun 26 2009 - 03:52:57 CDT)
- Re: [AMBER] installation of RESP programm FyD (Fri Jun 26 2009 - 04:15:39 CDT)
[AMBER] Problem with radial distribution function aneesh cna (Fri Jun 26 2009 - 03:56:09 CDT)
[AMBER] query about the charge fitting procedure about C- and N-terminal residues Ye MEI (Fri Jun 26 2009 - 04:19:47 CDT)
- Re: [AMBER] query about the charge fitting procedure about C- and N-terminal residues FyD (Fri Jun 26 2009 - 04:41:52 CDT)
[AMBER] a method or program to try to guess the net charge of a small molecule Alan (Fri Jun 26 2009 - 05:00:48 CDT)
[AMBER] force field choice ahmed said (Fri Jun 26 2009 - 03:21:16 CDT)
[AMBER] NAB memory E.M. (Fri Jun 26 2009 - 13:06:41 CDT)
- Re: [AMBER] NAB memory case (Fri Jun 26 2009 - 13:42:03 CDT)
[AMBER] explicit solvent NMR refinement Sally Pias (Sun Jun 28 2009 - 03:46:56 CDT)
- Re: [AMBER] explicit solvent NMR refinement Carlos Simmerling (Sun Jun 28 2009 - 07:36:42 CDT)
- Re: [AMBER] explicit solvent NMR refinement case (Sun Jun 28 2009 - 08:19:11 CDT)
[AMBER] Velocity rescaling and ig... Cihan Aydin (Sun Jun 28 2009 - 09:52:30 CDT)
- Re: [AMBER] Velocity rescaling and ig... Carlos Simmerling (Sun Jun 28 2009 - 10:35:37 CDT)
  - Re: [AMBER] Velocity rescaling and ig... Cihan Aydin (Sun Jun 28 2009 - 11:08:32 CDT)
    - RE: [AMBER] Velocity rescaling and ig... Ross Walker (Sun Jun 28 2009 - 11:18:08 CDT)
    - RE: [AMBER] Velocity rescaling and ig... Cihan Aydin (Sun Jun 28 2009 - 11:22:29 CDT)
[AMBER] how to creat an mixture sovlent of hexane and water TaoPaul (Sun Jun 28 2009 - 10:58:19 CDT)
[AMBER] Analysis of the solt-bridge Rilei Yu (Sun Jun 28 2009 - 17:24:28 CDT)
- Re: [AMBER] Analysis of the solt-bridge Alessandro Nascimento (Mon Jun 29 2009 - 07:58:49 CDT)
  - Re: [AMBER] Analysis of the solt-bridge Rilei Yu (Mon Jun 29 2009 - 17:42:23 CDT)
[AMBER] Simulations including RNA-protein complexes... Cihan Aydin (Sun Jun 28 2009 - 17:29:10 CDT)
[AMBER] RESP Syed Tarique Moin (Mon Jun 29 2009 - 02:42:51 CDT)
- Re: [AMBER] RESP case (Mon Jun 29 2009 - 06:52:19 CDT)
[AMBER] Steps for NMR structure minimization Prem Prakash Pathak (Mon Jun 29 2009 - 09:09:34 CDT)
- Re: [AMBER] Steps for NMR structure minimization case (Wed Jul 01 2009 - 07:48:13 CDT)
[AMBER] steps for NMR structure minimization of protein Prem Prakash Pathak (Mon Jun 29 2009 - 09:12:40 CDT)
[AMBER] steps for NMR structure minimization of protein Prem Prakash Pathak (Mon Jun 29 2009 - 09:13:33 CDT)
[AMBER] problems with ptraj option IMAGE Antonija TomiÄ‡ (Mon Jun 29 2009 - 09:48:54 CDT)
- Re: [AMBER] problems with ptraj option IMAGE Carlos Simmerling (Mon Jun 29 2009 - 10:00:59 CDT)
  - Re: [AMBER] problems with ptraj option IMAGE Antonija TomiÄ‡ (Mon Jun 29 2009 - 10:27:54 CDT)
[AMBER] Regd: parameter Fe4S4 KIRTANA S (Mon Jun 29 2009 - 11:11:49 CDT)
- Re: [AMBER] Regd: parameter Fe4S4 FyD (Mon Jun 29 2009 - 14:03:22 CDT)
[AMBER] Nonstandard molecules simulated with parm99EP ? Marek Maly (Mon Jun 29 2009 - 12:06:27 CDT)
- Re: [AMBER] Nonstandard molecules simulated with parm99EP ? FyD (Mon Jun 29 2009 - 13:28:19 CDT)
  - Re: [AMBER] Nonstandard molecules simulated with parm99EP ? Marek Maly (Mon Jun 29 2009 - 15:48:52 CDT)
[AMBER] Fe-S topology subarna thakur (Tue Jun 30 2009 - 01:29:16 CDT)
- Re: [AMBER] Fe-S topology Markus Kaukonen (Tue Jun 30 2009 - 02:28:51 CDT)
  - Re: [AMBER] Fe-S topology case (Tue Jun 30 2009 - 12:45:27 CDT)
[AMBER] Saccharides chains termini Sergey Samsonov (Tue Jun 30 2009 - 09:32:53 CDT)
- Re: [AMBER] Saccharides chains termini Lachele Foley (Lists) (Tue Jun 30 2009 - 09:46:09 CDT)
- Re: [AMBER] Saccharides chains termini Karl Kirschner (Tue Jun 30 2009 - 09:57:46 CDT)
- Re: [AMBER] Saccharides chains termini FyD (Tue Jun 30 2009 - 10:47:04 CDT)
[AMBER] Partial charges of heme Justine Shaw Condo (Tue Jun 30 2009 - 13:28:11 CDT)
[AMBER] Fe and Mn simulations Alessandro Nascimento (Tue Jun 30 2009 - 15:22:14 CDT)
[AMBER] antechamber R. A. (Wed Jul 01 2009 - 04:17:51 CDT)
- Re: [AMBER] antechamber Alan (Wed Jul 01 2009 - 06:37:40 CDT)
  - Re: [AMBER] antechamber case (Wed Jul 01 2009 - 07:04:02 CDT)
  - Re: [AMBER] antechamber gilbert_at_bluemarble.net (Wed Jul 01 2009 - 07:11:17 CDT)
    - Re: [AMBER] antechamber FyD (Wed Jul 01 2009 - 07:26:39 CDT)
[AMBER] antechamber R. A. (Wed Jul 01 2009 - 04:19:54 CDT)
- Re: [AMBER] antechamber R. A. (Wed Jul 01 2009 - 19:46:19 CDT)
  - Re: [AMBER] antechamber FyD (Thu Jul 02 2009 - 01:33:46 CDT)
    - Re: [AMBER] antechamber Alan (Thu Jul 02 2009 - 05:16:55 CDT)
- Re: [AMBER] antechamber R. A. (Thu Jul 02 2009 - 19:35:42 CDT)
  - »Ø¸´£º [AMBER] antechamber ÁÎÇà»ª (Thu Jul 02 2009 - 19:45:41 CDT)
    - å›žå¤ï¼š å›žå¤ï¼š [AMBER] antechamber å»–é’åŽ (Thu Jul 02 2009 - 19:53:06 CDT)
[AMBER] The problem of restart file Jeffrey (Wed Jul 01 2009 - 07:15:34 CDT)
- Re: [AMBER] The problem of restart file Carlos Simmerling (Wed Jul 01 2009 - 07:49:32 CDT)
- Re: [AMBER] The problem of restart file Jeffrey (Wed Jul 01 2009 - 09:07:08 CDT)
[AMBER] amber9 in fedora10 Bala subramanian (Wed Jul 01 2009 - 09:09:15 CDT)
- RE: [AMBER] amber9 in fedora10 Ross Walker (Wed Jul 01 2009 - 11:36:33 CDT)
  - Re: [AMBER] amber9 in fedora10 Bala subramanian (Thu Jul 02 2009 - 02:02:54 CDT)
    - Re: [AMBER] amber9 in fedora10 Bala subramanian (Thu Jul 02 2009 - 03:05:55 CDT)
[AMBER] pmemd/bintraj and ifort 10.1.0.21 Peter Varnai (Wed Jul 01 2009 - 13:28:30 CDT)
- Re: [AMBER] pmemd/bintraj and ifort 10.1.0.21 Robert Duke (Wed Jul 01 2009 - 13:54:52 CDT)
[AMBER] default integration scheme in 7 vs. 10 Paul Brandt (Wed Jul 01 2009 - 15:48:46 CDT)
- RE: [AMBER] default integration scheme in 7 vs. 10 Ross Walker (Wed Jul 01 2009 - 16:29:12 CDT)
- Re: [AMBER] default integration scheme in 7 vs. 10 case (Thu Jul 02 2009 - 06:37:17 CDT)
[AMBER] missing Halogen parameters (radii) for PBSA/GBSA calculations - PB Bomb in pb_aaradi(): No radius assigned for atom suhaib sh (Thu Jul 02 2009 - 08:18:05 CDT)
- å›žå¤ï¼š [AMBER] missing Halogen parameters (radii) for PBSA/GBSA calculations - PB Bomb in pb_aaradi(): No radius assigned for atom å»–é’åŽ (Thu Jul 02 2009 - 23:53:09 CDT)
[AMBER] analysis of QM/MM - LCOD Aust, Susanne (Fri Jul 03 2009 - 04:51:34 CDT)
[AMBER] MM-PBSA problem Giorgos Lamprinidis (Fri Jul 03 2009 - 08:50:36 CDT)
- Re: [AMBER] MM-PBSA problem Rubben Torella (Fri Jul 03 2009 - 08:57:09 CDT)
  - Re: [AMBER] MM-PBSA problem Giorgos Lamprinidis (Mon Jul 06 2009 - 03:07:14 CDT)
[AMBER] Re: Error in REDIII FyD (Fri Jul 03 2009 - 09:59:30 CDT)
[AMBER] calculation of the solvent accessibility Rilei Yu (Sat Jul 04 2009 - 03:54:23 CDT)
[AMBER] Boundary Condition Problem Pepe` Falahat (Sat Jul 04 2009 - 07:10:59 CDT)
- Re: [AMBER] Boundary Condition Problem case (Sat Jul 04 2009 - 08:45:45 CDT)
[AMBER] Leap Questions... Cihan Aydin (Sat Jul 04 2009 - 20:41:39 CDT)
- RE: [AMBER] Leap Questions... Ross Walker (Sun Jul 05 2009 - 23:01:34 CDT)
[AMBER] RED: Charge derivation of transtion state analogue manoj singh (Sun Jul 05 2009 - 01:10:57 CDT)
- Re: [AMBER] RED: Charge derivation of transtion state analogue FyD (Sun Jul 05 2009 - 04:39:13 CDT)
  - Re: [AMBER] RED: Charge derivation of transtion state analogue manoj singh (Mon Jul 06 2009 - 00:03:27 CDT)
    - Re: [AMBER] RED: Charge derivation of transtion state analogue FyD (Mon Jul 06 2009 - 01:29:11 CDT)
    - Re: [AMBER] RED: Charge derivation of transtion state analogue FyD (Mon Jul 06 2009 - 01:45:13 CDT)
[AMBER] Re: [q4md-fft] Charge calculation or non standard residue FyD (Sun Jul 05 2009 - 03:30:50 CDT)
[AMBER] RE: question about TUTORIAL A1 Ross Walker (Sun Jul 05 2009 - 21:29:38 CDT)
[AMBER] RE: ask for help (zn parameters) Ross Walker (Sun Jul 05 2009 - 21:56:50 CDT)
[AMBER] non standard residue Neha Gandhi (Mon Jul 06 2009 - 03:07:35 CDT)
- Re: [AMBER] non standard residue FyD (Tue Jul 07 2009 - 02:50:09 CDT)
- Re: [AMBER] non standard residue FyD (Tue Jul 14 2009 - 01:47:00 CDT)
- Re: [AMBER] non standard residue FyD (Tue Jul 14 2009 - 15:01:32 CDT)
[AMBER] Re: non aminoacid Residue Neha Gandhi (Mon Jul 06 2009 - 03:43:56 CDT)
- RE: [AMBER] Re: non aminoacid Residue Ross Walker (Mon Jul 06 2009 - 11:21:44 CDT)
[AMBER] unable to read MM charges Vishal Maingi (Mon Jul 06 2009 - 04:32:29 CDT)
[AMBER] need charges of FE-S cluster subarna thakur (Mon Jul 06 2009 - 05:44:05 CDT)
- Re: [AMBER] need charges of FE-S cluster case (Mon Jul 06 2009 - 07:35:19 CDT)
- Re: [AMBER] need charges of FE-S cluster Markus Kaukonen (Tue Jul 21 2009 - 13:50:39 CDT)
[AMBER] RE: question about TUTORIAL A1 Ross Walker (Mon Jul 06 2009 - 11:58:47 CDT)
[AMBER] unsolved verbosity when running minimization albert albert (Mon Jul 06 2009 - 14:09:02 CDT)
- Re: [AMBER] unsolved verbosity when running minimization Carlos Simmerling (Mon Jul 06 2009 - 14:28:08 CDT)
  - Re: [AMBER] unsolved verbosity when running minimization albert albert (Wed Jul 08 2009 - 06:10:43 CDT)
    - Re: [AMBER] unsolved verbosity when running minimization Carlos Simmerling (Wed Jul 08 2009 - 06:34:20 CDT)
[AMBER] Directory - GAFF Parameter File? Patrick Gedeon (Mon Jul 06 2009 - 18:31:49 CDT)
- [AMBER] Re: Directory - GAFF Parameter File? Patrick Gedeon (Mon Jul 06 2009 - 18:38:57 CDT)
[AMBER] RE: suggestions Ross Walker (Mon Jul 06 2009 - 20:01:51 CDT)
- Re: [AMBER] RE: suggestions Cihan Aydin (Mon Jul 06 2009 - 20:29:22 CDT)
[AMBER] Tleap input error, atom not found in residue template Brothers, Michael Charles (Mon Jul 06 2009 - 20:25:00 CDT)
- RE: [AMBER] Tleap input error, atom not found in residue template Ross Walker (Mon Jul 06 2009 - 23:28:46 CDT)
  - RE: [AMBER] Tleap input error, atom not found in residue template Brothers, Michael Charles (Tue Jul 07 2009 - 11:08:00 CDT)
  - [AMBER] Is rmsd ~ 3 A reasonable for a 4ns simulation? Catein Catherine (Wed Jul 08 2009 - 04:45:41 CDT)
[AMBER] unable to read MM charges (no reply yet) Vishal Maingi (Mon Jul 06 2009 - 22:32:07 CDT)
[AMBER] Principle Questions s_bill36_at_yahoo.co.uk (Tue Jul 07 2009 - 02:50:53 CDT)
- RE: [AMBER] Principle Questions Ross Walker (Tue Jul 07 2009 - 18:42:42 CDT)
[AMBER] DCCM Raja Pandian (Tue Jul 07 2009 - 06:05:20 CDT)
- RE: [AMBER] DCCM Duggan, Brendan M. (Wed Jul 15 2009 - 11:06:57 CDT)
[AMBER] Steered MD---more than one pair of atoms Hlengisizwe Ndlovu (Tue Jul 07 2009 - 08:27:59 CDT)
[AMBER] Zinc ion, help Mahmoud A. A. Ibrahim (Tue Jul 07 2009 - 09:26:48 CDT)
- Re: [AMBER] Zinc ion, help FyD (Wed Jul 08 2009 - 04:43:26 CDT)
[AMBER] rdparm bug? Paul Mortenson (Tue Jul 07 2009 - 11:29:44 CDT)
[AMBER] QMMM outupts Myeong Lee (Tue Jul 07 2009 - 12:13:27 CDT)
- Re: [AMBER] QMMM outupts Gustavo Seabra (Thu Jul 09 2009 - 11:58:30 CDT)
AW: [AMBER] Steered MD---more than one pair of atoms Aust, Susanne (Wed Jul 08 2009 - 01:47:56 CDT)
[AMBER] amber10 installation problem Lan JIN (Wed Jul 08 2009 - 01:49:05 CDT)
- Re: [AMBER] amber10 installation problem case (Wed Jul 08 2009 - 06:56:19 CDT)
- Re: [AMBER] amber10 installation problem Lan JIN (Wed Jul 08 2009 - 21:46:22 CDT)
  - Re: [AMBER] amber10 installation problem case (Thu Jul 09 2009 - 07:38:01 CDT)
- Re: [AMBER] amber10 installation problem Lan JIN (Fri Jul 10 2009 - 02:41:34 CDT)
[AMBER] Installing of amber10 Rilei Yu (Wed Jul 08 2009 - 03:34:24 CDT)
- Re: [AMBER] Installing of amber10 case (Wed Jul 08 2009 - 06:42:02 CDT)
[AMBER] installing of amber10 problem Rilei Yu (Wed Jul 08 2009 - 03:47:13 CDT)
[AMBER] MPI process terminated unexpectedly forrtl: error (69): process interrupted (SIGINT) Andrew Voronkov (Wed Jul 08 2009 - 04:39:03 CDT)
- Re: [AMBER] MPI process terminated unexpectedly forrtl: error (69): process interrupted (SIGINT) Andrew Voronkov (Wed Jul 08 2009 - 05:05:52 CDT)
- RE: [AMBER] MPI process terminated unexpectedly forrtl: error (69): process interrupted (SIGINT) Ross Walker (Wed Jul 08 2009 - 10:01:24 CDT)
[AMBER] suitable force field Jio M (Wed Jul 08 2009 - 05:06:35 CDT)
[AMBER] ouput trajectory of only CA atom Bala subramanian (Wed Jul 08 2009 - 08:24:56 CDT)
- Re: [AMBER] ouput trajectory of only CA atom Carlos Simmerling (Wed Jul 08 2009 - 09:41:25 CDT)
  - Re: [AMBER] ouput trajectory of only CA atom Bala subramanian (Wed Jul 08 2009 - 10:01:27 CDT)
    - Re: [AMBER] ouput trajectory of only CA atom Vlad Cojocaru (Wed Jul 08 2009 - 10:07:30 CDT)
    - Re: [AMBER] ouput trajectory of only CA atom Jordan Monnet (Wed Jul 08 2009 - 11:03:32 CDT)
[AMBER] ff parameters oguz gurbulak (Wed Jul 08 2009 - 09:35:40 CDT)
- Re: [AMBER] ff parameters case (Thu Jul 09 2009 - 08:23:31 CDT)
[AMBER] rmsd_dna balaji nagarajan (Wed Jul 08 2009 - 11:15:02 CDT)
- Re: [AMBER] rmsd_dna Carlos Simmerling (Wed Jul 08 2009 - 13:21:29 CDT)
  - RE: [AMBER] rmsd_dna balaji nagarajan (Wed Jul 08 2009 - 20:55:53 CDT)
[AMBER] bug in antechamber David Mobley (Wed Jul 08 2009 - 11:19:12 CDT)
- [AMBER] Re: bug in antechamber David Mobley (Mon Jul 13 2009 - 12:41:01 CDT)
[AMBER] suitable force field Jio M (Wed Jul 08 2009 - 02:14:12 CDT)
[AMBER] MM-PBSA delphi.crg and delphi.siz Manish Kumar (Wed Jul 08 2009 - 16:29:40 CDT)
- [AMBER] Re: MM-PBSA delphi.crg and delphi.siz Manish Kumar (Thu Jul 09 2009 - 22:33:01 CDT)
  - Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz suhaib sh (Fri Jul 10 2009 - 09:17:52 CDT)
  - Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz Ray Luo (Fri Jul 10 2009 - 11:32:18 CDT)
[AMBER] Acetylate and Amidate Alison Saunders (Wed Jul 08 2009 - 17:19:44 CDT)
- Re: [AMBER] Acetylate and Amidate Carlos Simmerling (Wed Jul 08 2009 - 17:22:58 CDT)
  - Re: [AMBER] Acetylate and Amidate Alison Saunders (Wed Jul 08 2009 - 17:47:59 CDT)
    - Re: [AMBER] Acetylate and Amidate Carlos Simmerling (Thu Jul 09 2009 - 06:52:28 CDT)
- Re: [AMBER] Acetylate and Amidate Bill Ross (Wed Jul 08 2009 - 18:13:09 CDT)
[AMBER] rmsd_ptraj balaji nagarajan (Wed Jul 08 2009 - 23:19:56 CDT)
- RE: [AMBER] rmsd_ptraj Ross Walker (Wed Jul 08 2009 - 23:35:59 CDT)
  - RE: [AMBER] rmsd_ptraj balaji nagarajan (Thu Jul 09 2009 - 00:50:10 CDT)
    - RE: [AMBER] rmsd_ptraj Thomas Cheatham (Thu Jul 09 2009 - 02:08:53 CDT)
[AMBER] charged or not s. Bill (Thu Jul 09 2009 - 07:33:05 CDT)
- Re: [AMBER] charged or not case (Thu Jul 09 2009 - 10:10:14 CDT)
[AMBER] Antechamber prep question Andrew Olson (Thu Jul 09 2009 - 09:39:25 CDT)
- Re: [AMBER] Antechamber prep question case (Thu Jul 09 2009 - 10:16:17 CDT)
- Re: [AMBER] Antechamber prep question Andrew Olson (Thu Jul 09 2009 - 10:22:18 CDT)
  - Re: [AMBER] Antechamber prep question case (Thu Jul 09 2009 - 11:48:44 CDT)
- Re: [AMBER] Antechamber prep question Andrew Olson (Thu Jul 09 2009 - 12:00:19 CDT)
  - Re: [AMBER] Antechamber prep question case (Thu Jul 09 2009 - 13:54:44 CDT)
    - Re: [AMBER] Antechamber prep question FyD (Fri Jul 10 2009 - 00:52:12 CDT)
    - Re: [AMBER] Antechamber prep question gilbert_at_bluemarble.net (Fri Jul 10 2009 - 08:10:32 CDT)
- Re: [AMBER] Antechamber prep question Andrew Olson (Fri Jul 10 2009 - 08:33:09 CDT)
  - Re: [AMBER] Antechamber prep question FyD (Fri Jul 10 2009 - 10:24:08 CDT)
[AMBER] Re: pls help and suggest Gustavo Seabra (Thu Jul 09 2009 - 11:14:42 CDT)
- Fw: [AMBER] Re: pls help and suggest Vishal Maingi (Thu Jul 09 2009 - 13:45:21 CDT)
  - Re: Fw: [AMBER] Re: pls help and suggest Gustavo Seabra (Fri Jul 17 2009 - 11:50:59 CDT)
[AMBER] reference re. determining size of timestep Paul Brandt (Thu Jul 09 2009 - 13:07:50 CDT)
- Re: [AMBER] reference re. determining size of timestep Gustavo Seabra (Fri Jul 17 2009 - 11:53:46 CDT)
[AMBER] AMBER windows version ? Siddharth Rastogi (Thu Jul 09 2009 - 16:14:05 CDT)
- RE: [AMBER] AMBER windows version ? Ross Walker (Thu Jul 09 2009 - 17:45:49 CDT)
  - Re: [AMBER] AMBER windows version ? Siddharth Rastogi (Thu Jul 09 2009 - 18:17:33 CDT)
[AMBER] question of mm_pbsa å»–é’åŽ (Thu Jul 09 2009 - 20:49:40 CDT)
- Re: [AMBER] question of mm_pbsa Hannes Kopitz (Fri Jul 10 2009 - 04:36:44 CDT)
  - å›žå¤ï¼š [AMBER] question of mm_pbsa å»–é’åŽ (Fri Jul 10 2009 - 19:50:55 CDT)
  - å›žå¤ï¼š [AMBER] question of mm_pbsa å»–é’åŽ (Fri Jul 10 2009 - 20:22:25 CDT)
- Re: [AMBER] question of mm_pbsa Ray Luo (Fri Jul 10 2009 - 11:47:12 CDT)
  - å›žå¤ï¼š [AMBER] question of mm_pbsa å»–é’åŽ (Sat Jul 11 2009 - 19:03:33 CDT)
[AMBER] unexplained blow-up at restart Sally Pias (Fri Jul 10 2009 - 03:02:42 CDT)
- Re: [AMBER] unexplained blow-up at restart Carlos Simmerling (Fri Jul 10 2009 - 05:55:51 CDT)
  - Re: [AMBER] unexplained blow-up at restart Sally Pias (Fri Jul 10 2009 - 10:29:01 CDT)
- Re: [AMBER] unexplained blow-up at restart Simon Becker (Fri Jul 10 2009 - 08:24:13 CDT)
[AMBER] Restrained backbone conformation MD simulation" Prem Prakash Pathak (Fri Jul 10 2009 - 06:27:38 CDT)
- Re: [AMBER] Restrained backbone conformation MD simulation" Carlos Simmerling (Fri Jul 10 2009 - 06:47:20 CDT)
[AMBER] manganese bondi radii for mm_pbsa calculation Chunliyan (Fri Jul 10 2009 - 08:39:51 CDT)
[AMBER] radius for Manganese ion Chunliyan (Fri Jul 10 2009 - 08:39:51 CDT)
[AMBER] Manganese Chunliyan (Fri Jul 10 2009 - 08:39:51 CDT)
[AMBER] Manganese bondi radii for mm/pbsa calculation Chunliyan (Fri Jul 10 2009 - 08:39:51 CDT)
[AMBER] Manganese bondi radii Chunliyan (Fri Jul 10 2009 - 08:39:51 CDT)
[AMBER] EPtot for Alpha-L- methyl fucose Sushil Mishra (Fri Jul 10 2009 - 08:47:26 CDT)
- Re: [AMBER] EPtot for Alpha-L- methyl fucose Carlos Simmerling (Fri Jul 10 2009 - 08:57:34 CDT)
  - Re: [AMBER] EPtot for Alpha-L- methyl fucose Sushil Mishra (Fri Jul 10 2009 - 09:12:28 CDT)
[AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10 Keith Van Nostrand (Fri Jul 10 2009 - 10:27:12 CDT)
- RE: [AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10 Ross Walker (Fri Jul 10 2009 - 11:21:11 CDT)
  - Re: [AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10 Keith Van Nostrand (Thu Jul 16 2009 - 16:08:04 CDT)
    - RE: [AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10 Ross Walker (Thu Jul 16 2009 - 22:34:13 CDT)
    - Re: [AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10 Keith Van Nostrand (Wed Jul 22 2009 - 10:58:08 CDT)
[AMBER] implicit solvent (GB version2) MD simulation workalemahu berhanu (Fri Jul 10 2009 - 10:53:47 CDT)
- Re: [AMBER] implicit solvent (GB version2) MD simulation Carlos Simmerling (Fri Jul 10 2009 - 10:57:57 CDT)
[AMBER] Need help for PMEMD 10 installation Jun Dong (Fri Jul 10 2009 - 11:05:49 CDT)
- RE: [AMBER] Need help for PMEMD 10 installation Ross Walker (Fri Jul 10 2009 - 11:26:29 CDT)
  - RE: [AMBER] Need help for PMEMD 10 installation Jun Dong (Fri Jul 10 2009 - 12:25:03 CDT)
[AMBER] problem with energy calculations Thomas Lake (Fri Jul 10 2009 - 11:13:55 CDT)
- Re: [AMBER] problem with energy calculations Carlos Simmerling (Fri Jul 10 2009 - 12:25:56 CDT)
  - RE: [AMBER] problem with energy calculations Lake, Thomas (Sun Jul 12 2009 - 08:35:33 CDT)
TMD: was: Re: [AMBER] charges in topology file Carlos Simmerling (Fri Jul 10 2009 - 11:36:30 CDT)
[AMBER] Peptide bond broken Syed Tarique Moin (Fri Jul 10 2009 - 13:19:02 CDT)
- Re: [AMBER] Peptide bond broken FyD (Sat Jul 11 2009 - 01:58:06 CDT)
- Re: [AMBER] Peptide bond broken case (Sun Jul 12 2009 - 21:35:35 CDT)
  - Re: [AMBER] Peptide bond broken Shubhra Gupta (Sun Jul 12 2009 - 23:17:31 CDT)
- Re: [AMBER] Peptide bond broken Syed Tarique Moin (Mon Jul 13 2009 - 08:20:02 CDT)
[AMBER] calculation of binding energy for lectin and fucuse.. Sushil Mishra (Fri Jul 10 2009 - 13:26:20 CDT)
[AMBER] ligand/protein minimization Andrew Olson (Fri Jul 10 2009 - 16:00:26 CDT)
- Re: [AMBER] ligand/protein minimization case (Sun Jul 12 2009 - 21:32:29 CDT)
- Re: [AMBER] ligand/protein minimization Andrew Olson (Mon Jul 13 2009 - 10:53:11 CDT)
  - Re: [AMBER] ligand/protein minimization case (Mon Jul 13 2009 - 11:29:06 CDT)
- Re: [AMBER] ligand/protein minimization Andrew Olson (Mon Jul 13 2009 - 12:10:18 CDT)
[AMBER] R.E.D intra-mcc and reorientation Ganesh Krishnan (Fri Jul 10 2009 - 17:00:35 CDT)
- Re: [AMBER] R.E.D intra-mcc and reorientation FyD (Sat Jul 11 2009 - 03:05:56 CDT)
  - Re: [AMBER] R.E.D intra-mcc and reorientation Ganesh Krishnan (Sat Jul 11 2009 - 17:56:18 CDT)
[AMBER] Syntax Bellymask Brothers, Michael Charles (Fri Jul 10 2009 - 18:59:01 CDT)
[AMBER] TMD: solvation and equilibration questions Jeffrey (Fri Jul 10 2009 - 20:07:55 CDT)
[AMBER] How to fix specific atoms? (not residue) Myeong Lee (Sat Jul 11 2009 - 06:46:06 CDT)
- Re: [AMBER] How to fix specific atoms? (not residue) Tom Joseph (Sat Jul 11 2009 - 17:01:04 CDT)
[AMBER] problem with the energetics of the system Mahmoud A. A. Ibrahim (Sat Jul 11 2009 - 18:23:13 CDT)
- Re: [AMBER] problem with the energetics of the system Ross Walker (Sat Jul 11 2009 - 18:52:42 CDT)
  - Re: [AMBER] problem with the energetics of the system Mahmoud A. A. Ibrahim (Sun Jul 12 2009 - 05:37:37 CDT)
[AMBER] amber dihedral format s. Bill (Sun Jul 12 2009 - 09:05:23 CDT)
- Re: [AMBER] amber dihedral format case (Sun Jul 12 2009 - 16:49:12 CDT)
[AMBER] help needed for HID s. Bill (Sun Jul 12 2009 - 13:16:08 CDT)
- Re: [AMBER] help needed for HID Marius Retegan (Sun Jul 12 2009 - 13:24:40 CDT)
- Re: [AMBER] help needed for HID FyD (Mon Jul 13 2009 - 15:27:13 CDT)
[AMBER] Amber10, Serial compilation with ifort Aldo Humberto Romero (Sun Jul 12 2009 - 15:57:40 CDT)
- RE: [AMBER] Amber10, Serial compilation with ifort Ross Walker (Sun Jul 12 2009 - 16:41:07 CDT)
[AMBER] ptraj mask selection Patrick Gedeon (Sun Jul 12 2009 - 22:45:56 CDT)
- Re: [AMBER] ptraj mask selection Jianyin Shao (Mon Jul 13 2009 - 12:57:23 CDT)
  - Re: [AMBER] ptraj mask selection case (Mon Jul 13 2009 - 13:10:46 CDT)
    - Re: [AMBER] ptraj mask selection Jianyin Shao (Mon Jul 13 2009 - 14:02:03 CDT)
    - Re: [AMBER] ptraj mask selection Patrick Gedeon (Mon Jul 13 2009 - 14:58:18 CDT)
[AMBER] Exclamation marks in trajectory Hugh Heldenbrand (Mon Jul 13 2009 - 10:16:26 CDT)
- RE: [AMBER] Exclamation marks in trajectory Ross Walker (Mon Jul 13 2009 - 13:13:17 CDT)
  - Re: [AMBER] Exclamation marks in trajectory Hugh Heldenbrand (Mon Jul 13 2009 - 13:52:37 CDT)
    - RE: [AMBER] Exclamation marks in trajectory Ross Walker (Mon Jul 13 2009 - 14:20:37 CDT)
[AMBER] Re: reference re. size of dt case (Mon Jul 13 2009 - 11:56:46 CDT)
[AMBER] Trouble saving amberparm files Alison Saunders (Mon Jul 13 2009 - 12:07:28 CDT)
- Re: [AMBER] Trouble saving amberparm files Tom Joseph (Mon Jul 13 2009 - 15:16:27 CDT)
  - Re: [AMBER] Trouble saving amberparm files Alison Saunders (Mon Jul 13 2009 - 16:06:12 CDT)
[AMBER] (no subject) Beale, John (Mon Jul 13 2009 - 12:35:46 CDT)
[AMBER] Problem with amber9 installation moitrayee_at_mbu.iisc.ernet.in (Mon Jul 13 2009 - 15:31:18 CDT)
- RE: [AMBER] Problem with amber9 installation Ross Walker (Mon Jul 13 2009 - 22:34:54 CDT)
  - RE: [AMBER] Problem with amber9 installation moitrayee_at_mbu.iisc.ernet.in (Tue Jul 14 2009 - 02:02:39 CDT)
[AMBER] GAFF and NME, ACE terminal res Jio M (Mon Jul 13 2009 - 15:51:06 CDT)
- Re: [AMBER] GAFF and NME, ACE terminal res FyD (Tue Jul 14 2009 - 02:40:00 CDT)
  - Re: [AMBER] GAFF and NME, ACE terminal res Jio M (Wed Jul 15 2009 - 23:29:08 CDT)
    - Re: [AMBER] GAFF and NME, ACE terminal res FyD (Thu Jul 16 2009 - 01:25:03 CDT)
[AMBER] Re: Request to mailing list AMBER rejected E.M. (Mon Jul 13 2009 - 22:37:46 CDT)
[AMBER] mpirun noticed that process rank 1 ... on signal 1 (Hangup). Naser Alijabbari (Tue Jul 14 2009 - 05:41:39 CDT)
- [AMBER] Re: mpirun noticed that process rank 1 ... on signal 1 (Hangup). Naser Alijabbari (Tue Jul 14 2009 - 05:49:14 CDT)
  - RE: [AMBER] Re: mpirun noticed that process rank 1 ... on signal 1 (Hangup). Ross Walker (Tue Jul 14 2009 - 07:33:49 CDT)
    - Re: [AMBER] Re: mpirun noticed that process rank 1 ... on signal 1 (Hangup). Naser Alijabbari (Tue Jul 14 2009 - 11:30:55 CDT)
[AMBER] RE: pmemd parallel Ross Walker (Tue Jul 14 2009 - 07:24:06 CDT)
- Re: [AMBER] RE: pmemd parallel Jun Dong (Wed Jul 15 2009 - 10:00:49 CDT)
[AMBER] Could not find bond parameter for O2 - ca Yogesh Aher (Tue Jul 14 2009 - 07:53:35 CDT)
- Re: [AMBER] Could not find bond parameter for O2 - ca case (Tue Jul 14 2009 - 22:28:02 CDT)
  - Re: [AMBER] Could not find bond parameter for O2 - ca Yogesh Aher (Fri Jul 17 2009 - 01:37:52 CDT)
[AMBER] Molecular Modeling Workshop and Model(l)ing'09 in Erlangen, Germany Harald Lanig (Tue Jul 14 2009 - 09:02:16 CDT)
[AMBER] Holding ligand rigid for minimization Andrew Olson (Tue Jul 14 2009 - 10:14:38 CDT)
[AMBER] Holding ligand rigid for minimization Andrew Olson (Tue Jul 14 2009 - 10:23:01 CDT)
- Re: [AMBER] Holding ligand rigid for minimization Andrew Olson (Tue Jul 14 2009 - 13:23:31 CDT)
[AMBER] PMEMD in a Cygwin Environment Hopkins, Robert (Tue Jul 14 2009 - 14:48:41 CDT)
- Re: [AMBER] PMEMD in a Cygwin Environment Robert Duke (Tue Jul 14 2009 - 15:16:46 CDT)
[AMBER] Counterion release and Free energy of binding ? Marek Maly (Tue Jul 14 2009 - 17:27:18 CDT)
- Re: [AMBER] Counterion release and Free energy of binding ? case (Tue Jul 14 2009 - 22:10:18 CDT)
  - Re: [AMBER] Counterion release and Free energy of binding ? Marek Maly (Fri Jul 17 2009 - 06:10:40 CDT)
[AMBER] Equilibrium water density Myeong Lee (Wed Jul 15 2009 - 03:58:52 CDT)
- Re: [AMBER] Equilibrium water density case (Wed Jul 15 2009 - 14:53:54 CDT)
[AMBER] Alpha-L-Methys Fucose structure problem bond 0fA.d.C1 OME.d.O "S" Sushil Mishra (Wed Jul 15 2009 - 05:36:26 CDT)
- Re: [AMBER] Alpha-L-Methys Fucose structure problem bond 0fA.d.C1 OME.d.O "S" Shubhra Gupta (Wed Jul 15 2009 - 07:38:34 CDT)
  - Re: [AMBER] Alpha-L-Methys Fucose structure problem bond 0fA.d.C1 OME.d.O "S" Sushil Mishra (Wed Jul 15 2009 - 08:58:13 CDT)
- Re: [AMBER] Alpha-L-Methys Fucose structure problem bond 0fA.d.C1 OME.d.O "S" Bill Ross (Wed Jul 15 2009 - 11:53:41 CDT)
[AMBER] Please help me out bharat lakhani (Wed Jul 15 2009 - 05:43:21 CDT)
- Re: [AMBER] Please help me out case (Wed Jul 15 2009 - 14:55:21 CDT)
[AMBER] R.E.D. help please s. Bill (Wed Jul 15 2009 - 09:11:46 CDT)
- Re: [AMBER] R.E.D. help please FyD (Wed Jul 15 2009 - 11:35:57 CDT)
[AMBER] position v time graph Shozeb Haider (Wed Jul 15 2009 - 13:21:35 CDT)
[AMBER] Can I get the torsion angle between base-pairs using ptraj ? Myeong Lee (Wed Jul 15 2009 - 16:51:02 CDT)
- Re: [AMBER] Can I get the torsion angle between base-pairs using ptraj ? Jordan Monnet (Wed Jul 15 2009 - 17:56:12 CDT)
[AMBER] different results for antechamber/mopac for the same input Alan (Wed Jul 15 2009 - 17:05:07 CDT)
- Re: [AMBER] different results for antechamber/mopac for the same input case (Thu Jul 16 2009 - 06:30:08 CDT)
[AMBER] ptraj - cluster Cihan Aydin (Thu Jul 16 2009 - 00:55:07 CDT)
- RE: [AMBER] ptraj - cluster Wei Huang (Fri Jul 17 2009 - 07:34:00 CDT)
  - RE: [AMBER] ptraj - cluster Cihan Aydin (Fri Jul 17 2009 - 09:22:37 CDT)
[AMBER] ptraj-radial distribution function Nancy (Thu Jul 16 2009 - 01:34:12 CDT)
- Re: [AMBER] ptraj-radial distribution function Christof Jaeger (Thu Jul 16 2009 - 03:22:02 CDT)
[AMBER] questions about RESP Jeffrey (Thu Jul 16 2009 - 01:57:28 CDT)
- Re: [AMBER] questions about RESP FyD (Thu Jul 16 2009 - 09:27:44 CDT)
- Re: [AMBER] questions about RESP Jeffrey (Mon Jul 20 2009 - 02:42:29 CDT)
  - Re: [AMBER] questions about RESP FyD (Mon Jul 20 2009 - 15:46:04 CDT)
- Re: [AMBER] questions about RESP Jeffrey (Thu Jul 23 2009 - 07:51:34 CDT)
  - Re: [AMBER] questions about RESP FyD (Thu Jul 23 2009 - 12:49:23 CDT)
    - Re: [AMBER] xleap installation error Bokun Cho (Mon Aug 03 2009 - 00:18:00 CDT)
    - Re: [AMBER] xleap installation error Scott Brozell (Mon Aug 03 2009 - 11:57:18 CDT)
[AMBER] carbonic anhydrase (CA) simulation vhakkim boy (Thu Jul 16 2009 - 02:03:23 CDT)
- Re: [AMBER] carbonic anhydrase (CA) simulation case (Thu Jul 16 2009 - 06:36:17 CDT)
[AMBER] command for RESP fitting bharat lakhani (Thu Jul 16 2009 - 02:10:33 CDT)
- Re: [AMBER] command for RESP fitting FyD (Thu Jul 16 2009 - 09:34:28 CDT)
  - Re: [AMBER] command for RESP fitting bharat lakhani (Mon Jul 20 2009 - 02:01:23 CDT)
[AMBER] query regarding FE4S4 subarna thakur (Thu Jul 16 2009 - 02:14:27 CDT)
- Re: [AMBER] query regarding FE4S4 case (Thu Jul 16 2009 - 06:45:06 CDT)
[AMBER] Coordinate resetting (SHAKE) cannot be accomplished, Zhongjie Liang (Thu Jul 16 2009 - 03:37:29 CDT)
- Re: [AMBER] Coordinate resetting (SHAKE) cannot be accomplished, steinbrt_at_rci.rutgers.edu (Thu Jul 16 2009 - 04:01:15 CDT)
  - ´ð¸´: [AMBER] Coordinate resetting (SHAKE) cannot be accomplished, Zhongjie Liang (Thu Jul 16 2009 - 04:16:02 CDT)
[AMBER] IDIVF and PN s. Bill (Thu Jul 16 2009 - 07:11:27 CDT)
- RE: [AMBER] IDIVF and PN Ross Walker (Thu Jul 16 2009 - 22:40:11 CDT)
[AMBER] production phase s. Bill (Thu Jul 16 2009 - 07:18:25 CDT)
- RE: [AMBER] production phase Ross Walker (Thu Jul 16 2009 - 22:56:13 CDT)
[AMBER] vlimit exceeded....nscu_SMD!! Hlengisizwe Ndlovu (Thu Jul 16 2009 - 07:53:50 CDT)
[AMBER] Disappearing common atoms in Amber 10 with TI Khavrutskii, Ilja (Thu Jul 16 2009 - 08:38:43 CDT)
- Re: [AMBER] Disappearing common atoms in Amber 10 with TI steinbrt_at_rci.rutgers.edu (Thu Jul 16 2009 - 09:09:39 CDT)
  - Re: [AMBER] Disappearing common atoms in Amber 10 with TI Khavrutskii, Ilja (Thu Jul 16 2009 - 16:02:10 CDT)
[AMBER] ntt=3 and ibelly=1 Kristina Furse (Thu Jul 16 2009 - 11:07:23 CDT)
- RE: [AMBER] ntt=3 and ibelly=1 Ross Walker (Thu Jul 16 2009 - 22:44:47 CDT)
  - RE: [AMBER] ntt=3 and ibelly=1 Kristina Furse (Fri Jul 17 2009 - 11:41:29 CDT)
[AMBER] amino acids caps for truncated proteins Andrew Voronkov (Thu Jul 16 2009 - 11:31:18 CDT)
- Re: [AMBER] amino acids caps for truncated proteins FyD (Thu Jul 16 2009 - 11:58:32 CDT)
[AMBER] Umbrella Sampling Hemant Kumar (Thu Jul 16 2009 - 13:01:40 CDT)
- Re: [AMBER] Umbrella Sampling case (Thu Jul 16 2009 - 15:03:29 CDT)
  - RE: [AMBER] Umbrella Sampling Seetin, Matthew (Thu Jul 16 2009 - 15:13:59 CDT)
    - RE: [AMBER] Umbrella Sampling Hemant Kumar (Sat Jul 18 2009 - 14:28:19 CDT)
[AMBER] amber10 parallel compiling error Nam Kim (Thu Jul 16 2009 - 19:50:57 CDT)
- å›žå¤ï¼š [AMBER] amber10 parallel compiling error å»–é’åŽ (Thu Jul 16 2009 - 20:27:05 CDT)
- RE: [AMBER] amber10 parallel compiling error Ross Walker (Thu Jul 16 2009 - 22:43:15 CDT)
- Re: [AMBER] amber10 parallel compiling error nam kim (Mon Jul 20 2009 - 12:24:14 CDT)
  - RE: [AMBER] amber10 parallel compiling error Ross Walker (Mon Jul 20 2009 - 12:33:08 CDT)
[AMBER] File conversion for from Amber to Charmm Yogesh Aher (Fri Jul 17 2009 - 01:45:11 CDT)
- Re: [AMBER] File conversion for from Amber to Charmm case (Fri Jul 17 2009 - 06:53:06 CDT)
[AMBER] diffusion coeficients felix (Fri Jul 17 2009 - 03:15:35 CDT)
- Re: [AMBER] diffusion coeficients case (Fri Jul 17 2009 - 06:59:41 CDT)
  - Re: [AMBER] diffusion coeficients felix (Fri Jul 17 2009 - 08:41:43 CDT)
[AMBER] Steered MD.....SHAKE error!! Hlengisizwe Ndlovu (Fri Jul 17 2009 - 03:50:11 CDT)
- Re: [AMBER] Steered MD.....SHAKE error!! case (Fri Jul 17 2009 - 07:01:03 CDT)
[AMBER] vlimit error after heating restart AL Olson (Fri Jul 17 2009 - 09:26:05 CDT)
[AMBER] The Right Neutralization Procedure and Ionic Strength Calculation ? Marek Maly (Fri Jul 17 2009 - 11:34:44 CDT)
- Re: [AMBER] The Right Neutralization Procedure and Ionic Strength Calculation ? Thomas Cheatham III (Fri Jul 17 2009 - 11:50:15 CDT)
  - Re: [AMBER] The Right Neutralization Procedure and Ionic Strength Calculation ? Marek Maly (Fri Jul 17 2009 - 13:37:02 CDT)
- Re: [AMBER] The Right Neutralization Procedure and Ionic Strength Calculation ? Andrew Voronkov (Tue Jul 28 2009 - 23:19:41 CDT)
[AMBER] RESP fit E.M. (Fri Jul 17 2009 - 18:00:08 CDT)
- Re: [AMBER] RESP fit FyD (Sat Jul 18 2009 - 01:29:56 CDT)
[AMBER] charge not zero on group: RESP Jio M (Sat Jul 18 2009 - 00:14:58 CDT)
- Re: [AMBER] charge not zero on group: RESP Ben Roberts (Sat Jul 18 2009 - 07:45:10 CDT)
[AMBER] RE: charge not zero on group:''''.respin1 attached Jio M (Sat Jul 18 2009 - 09:40:18 CDT)
- Re: [AMBER] RE: charge not zero on group:''''.respin1 attached FyD (Sun Jul 19 2009 - 02:41:17 CDT)
[AMBER] amber10 parallel compiling error nam kim (Sat Jul 18 2009 - 12:19:39 CDT)
[AMBER] Box shape change Hemant Kumar (Sat Jul 18 2009 - 14:38:46 CDT)
- Re: [AMBER] Box shape change Carlos Simmerling (Sat Jul 18 2009 - 20:35:41 CDT)
  - Re: [AMBER] Box shape change Hemant Kumar (Sun Jul 19 2009 - 06:00:18 CDT)
[AMBER] Different machines s. Bill (Sun Jul 19 2009 - 04:55:48 CDT)
- RE: [AMBER] Different machines Ross Walker (Sun Jul 19 2009 - 11:28:52 CDT)
[AMBER] -a flag :RESP Jio M (Sun Jul 19 2009 - 05:48:20 CDT)
[AMBER] which keyword s. Bill (Sun Jul 19 2009 - 07:21:23 CDT)
[AMBER] (no subject) gunajyoti das (Sun Jul 19 2009 - 10:14:20 CDT)
- Re: [AMBER] setting AMBERHOME case (Wed Jul 22 2009 - 21:15:34 CDT)
[AMBER] (no subject) gunajyoti das (Sun Jul 19 2009 - 10:13:01 CDT)
[AMBER] Tutorial A3 s. Bill (Sun Jul 19 2009 - 14:33:58 CDT)
- RE: [AMBER] Tutorial A3 Ross Walker (Mon Jul 20 2009 - 14:03:44 CDT)
[AMBER] bugfix 10 failing for ambertools1.2 Alan (Mon Jul 20 2009 - 03:14:16 CDT)
- [AMBER] Re: bugfix 10 failing for ambertools1.2 Alan (Mon Jul 20 2009 - 03:25:55 CDT)
  - Re: [AMBER] Re: bugfix 10 failing for ambertools1.2 case (Mon Jul 27 2009 - 10:03:24 CDT)
[AMBER] nasty memory bug in calculatePrincipalAxis Hannes Loeffler (Mon Jul 20 2009 - 03:30:38 CDT)
- Re: [AMBER] nasty memory bug in calculatePrincipalAxis Scott Brozell (Mon Oct 12 2009 - 16:38:06 CDT)
[AMBER] MM-PBSA tail: equil.out: file truncated during equilibration of salivated complex Sushil Mishra (Mon Jul 20 2009 - 03:32:32 CDT)
[AMBER] Output file truncated during equilibration of salivated complex in MM-PBSA Sushil Mishra (Mon Jul 20 2009 - 05:40:51 CDT)
[AMBER] file truncated : Output file truncated during equilibration of salivated complex in MM-PBSA Sushil Mishra (Mon Jul 20 2009 - 07:26:27 CDT)
[AMBER] RE: DCCM Duggan, Brendan M. (Mon Jul 20 2009 - 09:29:46 CDT)
[AMBER] nonbon.f question Rizwan Tai (Mon Jul 20 2009 - 14:31:17 CDT)
[AMBER] RE: the copper paramter Ross Walker (Mon Jul 20 2009 - 16:38:14 CDT)
[AMBER] equivalent atoms Ye MEI (Mon Jul 20 2009 - 23:56:52 CDT)
[AMBER] ptraj grid option Youn Kyeung Lee (Tue Jul 21 2009 - 02:15:11 CDT)
[AMBER] Output forces in Sander Frank X. Vázquez (Tue Jul 21 2009 - 16:58:36 CDT)
- Re: [AMBER] Output forces in Sander case (Mon Jul 27 2009 - 10:11:30 CDT)
[AMBER] Compiling Amber 10 (serial) on Mac OS X 10.5.7 w/ gcc, Intel Fortan 11.0 and MKL 10.0 David Watson (Tue Jul 21 2009 - 16:20:36 CDT)
- Re: [AMBER] Compiling Amber 10 (serial) on Mac OS X 10.5.7 w/ gcc, Intel Fortan 11.0 and MKL 10.0 Scott Brozell (Wed Jul 22 2009 - 14:52:59 CDT)
[AMBER] RE: Questions about QMMM Ross Walker (Tue Jul 21 2009 - 17:47:49 CDT)
[AMBER] Patching terminal Manish Kumar (Tue Jul 21 2009 - 18:53:54 CDT)
=?utf-8?B?UmU6IFtBTUJFUl0gQ29tcGlsaW5nIEFtYmVyIDEwIChzZXJpYWwpIG9uIE1hYyBPUyBYIDEwLjUuNyB3LyBnY2MsCUludGVsIEZvcnRhbiAxMS4wIGFuZCBNS0wgMTAuMA==?= vitor.felix (Tue Jul 21 2009 - 22:15:06 CDT)
[AMBER] ESP charges of Fe4S4 subarna thakur (Wed Jul 22 2009 - 00:19:48 CDT)
[AMBER] Regarding Hbond interactions aneesh cna (Wed Jul 22 2009 - 01:30:10 CDT)
- Re: [AMBER] Regarding Hbond interactions Thomas Cheatham (Thu Jul 23 2009 - 17:57:57 CDT)
[AMBER] Equilibration step Olotu Odunayo (Wed Jul 22 2009 - 04:47:37 CDT)
- Re: [AMBER] Equilibration step Tom Joseph (Wed Jul 22 2009 - 07:35:15 CDT)
  - RE: [AMBER] Equilibration step Olotu Odunayo (Wed Jul 22 2009 - 11:41:13 CDT)
    - Re: [AMBER] Equilibration step Tom Joseph (Wed Jul 22 2009 - 14:05:58 CDT)
    - RE: [AMBER] Equilibration step Olotu Odunayo (Thu Jul 23 2009 - 01:52:50 CDT)
  - RE: [AMBER] Equilibration step Olotu Odunayo (Wed Jul 22 2009 - 11:46:12 CDT)
[AMBER] errors of PMEMD installation å»–é’åŽ (Wed Jul 22 2009 - 09:28:45 CDT)
- Re: [AMBER] errors of PMEMD installation Mengjuei Hsieh (Thu Jul 23 2009 - 14:25:27 CDT)
  - å›žå¤ï¼š [AMBER] errors of PMEMD installation å»–é’åŽ (Thu Jul 23 2009 - 20:27:51 CDT)
[AMBER] saquinavir parameterization with antechamber Oliver Kuhn (Wed Jul 22 2009 - 10:42:49 CDT)
- Re: [AMBER] saquinavir parameterization with antechamber FyD (Wed Jul 22 2009 - 13:41:21 CDT)
  - Re: [AMBER] saquinavir parameterization with antechamber Oliver Kuhn (Thu Jul 23 2009 - 02:02:49 CDT)
    - Re: [AMBER] saquinavir parameterization with antechamber FyD (Thu Jul 23 2009 - 02:29:57 CDT)
    - Re: [AMBER] saquinavir parameterization with antechamber Oliver Kuhn (Thu Jul 23 2009 - 03:06:00 CDT)
[AMBER] [ALERT]: It's the time to come out on streets and stop the complete nation on it's place - Take immediate actions at once with full force. Organization (Wed Jul 22 2009 - 14:13:37 CDT)
[AMBER] how to launch XLEaP from SSH Secure Shell? Yana Berezovskaya (Wed Jul 22 2009 - 17:44:45 CDT)
- Re: [AMBER] how to launch XLEaP from SSH Secure Shell? Robert Duke (Wed Jul 22 2009 - 18:07:24 CDT)
  - Re: [AMBER] how to launch XLEaP from SSH Secure Shell? Tom Joseph (Wed Jul 22 2009 - 18:24:56 CDT)
    - Re: [AMBER] how to launch XLEaP from SSH Secure Shell? David Watson (Wed Jul 22 2009 - 19:30:12 CDT)
    - Re: [AMBER] how to launch XLEaP from SSH Secure Shell? Thomas Patko (Wed Jul 22 2009 - 19:47:51 CDT)
[AMBER] Replacing DNA base with analog amoreno_at_wesleyan.edu (Thu Jul 23 2009 - 09:20:08 CDT)
- RE: [AMBER] Replacing DNA base with analog Kristina Furse (Thu Jul 23 2009 - 09:36:26 CDT)
[AMBER] Compiling AMBER 10 (parallel, MPICH2) on Mac OS X Intel w/gcc, ifort, icc David Watson (Thu Jul 23 2009 - 15:03:59 CDT)
RE: [Subject Filtered] Re: [AMBER] PMEMD in a Cygwin Environment 8% Hopkins, Robert (Thu Jul 23 2009 - 15:37:12 CDT)
[AMBER] Langevin Dynamics in AMBER10 Biswaranjan Meher (Thu Jul 23 2009 - 16:54:58 CDT)
- Re: [AMBER] Langevin Dynamics in AMBER10 Carlos Simmerling (Thu Jul 23 2009 - 16:57:44 CDT)
  - Re: [AMBER] Langevin Dynamics in AMBER10 Biswaranjan Meher (Thu Jul 23 2009 - 18:12:59 CDT)
    - Re: [AMBER] Langevin Dynamics in AMBER10 Carlos Simmerling (Fri Jul 24 2009 - 07:01:28 CDT)
[AMBER] mailing list Qinghua Liao (Thu Jul 23 2009 - 20:45:50 CDT)
[AMBER] radical simulation Jeffrey (Fri Jul 24 2009 - 02:34:53 CDT)
- Re: [AMBER] radical simulation Manish Kumar (Fri Jul 24 2009 - 02:48:01 CDT)
- Re: [AMBER] radical simulation FyD (Fri Jul 24 2009 - 05:27:34 CDT)
- Re: [AMBER] radical simulation Jeffrey (Sun Jul 26 2009 - 07:28:39 CDT)
[AMBER] xleap facility to insert a residue Sergey Samsonov (Fri Jul 24 2009 - 08:07:27 CDT)
[AMBER] thymidine monophosphate parametrization Yvonne.Westermaier_at_unige.ch (Fri Jul 24 2009 - 10:18:18 CDT)
- Re: [AMBER] thymidine monophosphate parametrization case (Mon Jul 27 2009 - 09:47:38 CDT)
  - Re: [AMBER] thymidine monophosphate parametrization Yvonne.Westermaier_at_unige.ch (Tue Jul 28 2009 - 07:10:43 CDT)
[AMBER] loading a mol2 file in xleap vallespardojl_at_chem.leidenuniv.nl (Fri Jul 24 2009 - 12:40:13 CDT)
- Re: [AMBER] loading a mol2 file in xleap FyD (Fri Jul 24 2009 - 15:00:41 CDT)
  - Re: [AMBER] loading a mol2 file in xleap vallespardojl_at_chem.leidenuniv.nl (Mon Jul 27 2009 - 07:40:13 CDT)
    - Re: [AMBER] loading a mol2 file in xleap FyD (Mon Jul 27 2009 - 08:44:50 CDT)
- [AMBER] Could not find type: MG Parameter file was not saved. Mannan (Sat Jul 25 2009 - 22:41:24 CDT)
  - [AMBER] Could not find type: MG Parameter file was not saved. though it was loaded Mannan (Sun Jul 26 2009 - 22:49:54 CDT)
    - Re: [AMBER] Could not find type: MG Parameter file was not saved. though it was loaded FyD (Mon Jul 27 2009 - 00:03:00 CDT)
[AMBER] DNA + intercalator Rodrigo Galindo (Fri Jul 24 2009 - 17:22:35 CDT)
Re: [AMBER] DNA + intercalator Bill Ross (Fri Jul 24 2009 - 18:03:06 CDT)
- Re: [AMBER] DNA + intercalator Ashish Runthala (Fri Jul 24 2009 - 22:12:27 CDT)
[AMBER] Simulation with United atom force field in Implicit solvent. Manish Kumar (Sat Jul 25 2009 - 22:55:42 CDT)
- Re: [AMBER] Simulation with United atom force field in Implicit solvent. Ray Luo (Sun Jul 26 2009 - 02:09:07 CDT)
  - Re: [AMBER] Simulation with United atom force field in Implicit solvent. Manish Kumar (Sun Jul 26 2009 - 13:22:40 CDT)
[AMBER] Removed proton in protein (Advanced Tutorials A1 old) albert albert (Mon Jul 27 2009 - 01:57:20 CDT)
- Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old) Ashish Runthala (Mon Jul 27 2009 - 04:09:23 CDT)
- Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old) Bill Ross (Mon Jul 27 2009 - 11:17:29 CDT)
  - Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old) Ashish Runthala (Tue Jul 28 2009 - 05:28:40 CDT)
[AMBER] How to read md trajectory for each time slice as an input coordinate Myeong Lee (Mon Jul 27 2009 - 03:16:47 CDT)
[AMBER] error in antechamber Qinghua Liao (Mon Jul 27 2009 - 06:57:50 CDT)
- Re: [AMBER] error in antechamber Mengjuei Hsieh (Mon Jul 27 2009 - 17:29:06 CDT)
  - Re: [AMBER] error in antechamber Qinghua Liao (Mon Jul 27 2009 - 20:02:26 CDT)
    - Re: [AMBER] error in antechamber case (Mon Jul 27 2009 - 23:23:54 CDT)
    - Re: [AMBER] error in antechamber Qinghua Liao (Tue Jul 28 2009 - 00:13:49 CDT)
[AMBER] Average structure over simulation Olotu Odunayo (Mon Jul 27 2009 - 08:38:59 CDT)
- [AMBER] RE: Average structure over simulation Niel Henriksen (Mon Jul 27 2009 - 09:56:40 CDT)
  - RE: [AMBER] RE: Average structure over simulation Olotu Odunayo (Mon Jul 27 2009 - 10:47:20 CDT)
[AMBER] residues lacking connect0/connect1 Jio M (Mon Jul 27 2009 - 11:10:06 CDT)
Re: [AMBER] residues lacking connect0/connect1 Bill Ross (Mon Jul 27 2009 - 11:40:31 CDT)
[AMBER] nonbon.f question Rizwan Tai (Mon Jul 27 2009 - 14:30:12 CDT)
- Re: [AMBER] nonbon.f question Carlos Simmerling (Mon Jul 27 2009 - 14:34:20 CDT)
  - Re: [AMBER] nonbon.f question Rizwan Tai (Mon Aug 03 2009 - 11:13:21 CDT)
    - RE: [AMBER] nonbon.f question Ross Walker (Mon Aug 03 2009 - 13:32:18 CDT)
[AMBER] Using idecomp=3 with igb=10 (PB) Chris Whittleston (Mon Jul 27 2009 - 15:04:14 CDT)
- Re: [AMBER] Using idecomp=3 with igb=10 (PB) Hannes Kopitz (Tue Jul 28 2009 - 05:09:01 CDT)
  - Re: [AMBER] Using idecomp=3 with igb=10 (PB) Chris Whittleston (Tue Jul 28 2009 - 05:54:09 CDT)
[AMBER] QM/MM s. Bill (Tue Jul 28 2009 - 01:44:15 CDT)
- RE: [AMBER] QM/MM Syed Tarique Moin (Mon May 04 2009 - 17:13:22 CDT)
  - RE: [AMBER] QM/MM Ross Walker (Tue May 05 2009 - 17:16:26 CDT)
- RE: [AMBER] QM/MM Syed Tarique Moin (Wed May 06 2009 - 02:11:54 CDT)
- RE: [AMBER] QM/MM Syed Tarique Moin (Wed May 06 2009 - 02:12:17 CDT)
- Re: [AMBER] QM/MM steinbrt_at_rci.rutgers.edu (Tue Jul 28 2009 - 02:19:32 CDT)
[AMBER] PLUMED release 1.1.0 available Massimiliano Bonomi (Tue Jul 28 2009 - 03:10:39 CDT)
- [AMBER] How to visualize PCA results without IED? Catein Catherine (Tue Jul 28 2009 - 04:30:22 CDT)
[AMBER] RE: MM-PBSA test jobs error messages Catein Catherine (Tue Jul 28 2009 - 04:24:31 CDT)
[AMBER] pulling two atoms in SMD Santosh Mogurampelly (Tue Jul 28 2009 - 07:10:12 CDT)
[AMBER] Error in Sander Output File Alison Saunders (Tue Jul 28 2009 - 12:00:12 CDT)
[AMBER] Am I doing the right thing nicholus bhattacharjee (Tue Jul 28 2009 - 12:20:57 CDT)
- Re: [AMBER] Am I doing the right thing Ashish Runthala (Tue Jul 28 2009 - 20:35:09 CDT)
- Re: [AMBER] Am I doing the right thing Bill Ross (Tue Jul 28 2009 - 21:39:48 CDT)
  - Re: [AMBER] Am I doing the right thing Ashish Runthala (Tue Jul 28 2009 - 22:44:59 CDT)
    - Re: [AMBER] Am I doing the right thing nicholus bhattacharjee (Tue Jul 28 2009 - 23:36:31 CDT)
[AMBER] Question on REST and VALUE1 keywords hwu_at_clarku.edu (Tue Jul 28 2009 - 16:06:34 CDT)
- Re: [AMBER] Question on REST and VALUE1 keywords Carlos Simmerling (Tue Jul 28 2009 - 16:14:20 CDT)
  - Re: [AMBER] Question on REST and VALUE1 keywords Ashish Runthala (Tue Jul 28 2009 - 20:26:19 CDT)
[AMBER] how to choose exclusion policy for GPCR xueqin pang (Tue Jul 28 2009 - 21:12:33 CDT)
[AMBER] RE: MM-PBSA test jobs error messages (with bugfix.all) Catein Catherine (Wed Jul 29 2009 - 00:50:50 CDT)
[AMBER] pdb file no bond and charges Jio M (Wed Jul 29 2009 - 01:28:48 CDT)
[AMBER] RED.III: Invalid Optimization OUTPUT s. Bill (Wed Jul 29 2009 - 03:37:27 CDT)
- Re: Solved it thanks [AMBER] RED.III: Invalid Optimization OUTPUT s. Bill (Wed Jul 29 2009 - 07:14:02 CDT)
[AMBER] Re: MM-PBSA test jobs error messages (Can i fix the problem without recompile the amber?) Catein Catherine (Wed Jul 29 2009 - 04:39:02 CDT)
[AMBER] MPI error vhakkim boy (Wed Jul 29 2009 - 04:44:35 CDT)
- Re: [AMBER] MPI error Robert Duke (Wed Jul 29 2009 - 07:05:57 CDT)
[AMBER] MM/PBSA, MM/GBSA and NMODE Analysis Matthias Negri (Wed Jul 29 2009 - 05:55:46 CDT)
- Re: [AMBER] MM/PBSA, MM/GBSA and NMODE Analysis Ray Luo (Wed Jul 29 2009 - 19:25:14 CDT)
[AMBER] Compiling AmberTools 1.2 with intel compilers for Mac Osx in 64 bits Alan (Wed Jul 29 2009 - 11:00:42 CDT)
- Re: [AMBER] Compiling AmberTools 1.2 with intel compilers for Mac Osx in 64 bits David Watson (Wed Jul 29 2009 - 11:21:50 CDT)
  - Re: [AMBER] Compiling AmberTools 1.2 with intel compilers for Mac Osx in 64 bits Alan (Thu Jul 30 2009 - 08:39:03 CDT)
    - Re: [AMBER] Compiling AmberTools 1.2 with intel compilers for Mac Osx in 64 bits David Watson (Thu Jul 30 2009 - 14:10:39 CDT)
[AMBER] Installing Amber10 on Ubuntu David Dubins (Wed Jul 29 2009 - 13:50:12 CDT)
- Re: [AMBER] Installing Amber10 on Ubuntu Rodrigo Galindo (Wed Jul 29 2009 - 14:49:33 CDT)
[AMBER] Re: problem of installation of amber10 Mengjuei Hsieh (Wed Jul 29 2009 - 14:41:52 CDT)
[AMBER] Normal mode analysis of water bharat lakhani (Thu Jul 30 2009 - 04:27:19 CDT)
- Re: [AMBER] Normal mode analysis of water case (Thu Jul 30 2009 - 09:11:23 CDT)
[AMBER] PCA analysis: the first vector is the movement of whole molecule. Catein Catherine (Thu Jul 30 2009 - 05:37:49 CDT)
- Re: [AMBER] PCA analysis: the first vector is the movement of whole molecule. Hannes Loeffler (Thu Jul 30 2009 - 05:52:48 CDT)
  - RE: [AMBER] PCA analysis: the first vector is the movement of whole molecule. Catein Catherine (Thu Jul 30 2009 - 22:46:49 CDT)
    - RE: [AMBER] PCA analysis: the first vector is the movement of whole molecule. Hannes Loeffler (Fri Jul 31 2009 - 02:27:54 CDT)
    - RE: [AMBER] PCA analysis: the first vector is the movement of whole molecule. Catein Catherine (Sun Aug 02 2009 - 22:47:07 CDT)
[AMBER] ambpdb problem Jio M (Thu Jul 30 2009 - 14:12:10 CDT)
- Re: [AMBER] ambpdb problem Jordan Monnet (Thu Jul 30 2009 - 14:32:57 CDT)
  - Re: [AMBER] ambpdb problem Ashish Runthala (Thu Jul 30 2009 - 22:44:10 CDT)
- Re: [AMBER] ambpdb problem Jio M (Fri Jul 31 2009 - 02:11:32 CDT)
  - Re: [AMBER] ambpdb problem Jordan Monnet (Fri Jul 31 2009 - 09:30:54 CDT)
    - Re: [AMBER] ambpdb problem Ashish Runthala (Fri Jul 31 2009 - 20:28:42 CDT)
[AMBER] Non-Standard Amino Acid Residue LEAP ERROR Brothers, Michael Charles (Thu Jul 30 2009 - 17:28:43 CDT)
- Re: [AMBER] Non-Standard Amino Acid Residue LEAP ERROR Ashish Runthala (Thu Jul 30 2009 - 22:40:45 CDT)
  - RE: [AMBER] Non-Standard Amino Acid Residue LEAP ERROR Brothers, Michael Charles (Fri Jul 31 2009 - 12:36:10 CDT)
    - Re: [AMBER] Non-Standard Amino Acid Residue LEAP ERROR Ashish Runthala (Fri Jul 31 2009 - 20:39:54 CDT)
[AMBER] What is the meaning of "rms first *" Catein Catherine (Thu Jul 30 2009 - 22:49:17 CDT)
[AMBER] query bharat lakhani (Fri Jul 31 2009 - 02:42:04 CDT)
- [AMBER] Re: query bharat lakhani (Sat Aug 01 2009 - 07:07:24 CDT)
  - Re: [AMBER] Re: query Ashish Runthala (Sat Aug 01 2009 - 07:21:47 CDT)
[AMBER] Compilation error with pmemd (amber10) on fedora9 64 bits Nicolas SAPAY (Fri Jul 31 2009 - 04:41:21 CDT)
- Re: [AMBER] Compilation error with pmemd (amber10) on fedora9 64 bits Robert Duke (Fri Jul 31 2009 - 07:33:52 CDT)
  - Re: [AMBER] Compilation error with pmemd (amber10) on fedora9 64 bits Nicolas SAPAY (Fri Jul 31 2009 - 07:55:18 CDT)
[AMBER] vertex atom mismatch Clark, Tiffany D (Fri Jul 31 2009 - 08:14:15 CDT)
- Re: [AMBER] vertex atom mismatch Guillermo Mulliert Carlín (Fri Jul 31 2009 - 09:33:46 CDT)
[AMBER] problem from xleap Qinghua Liao (Fri Jul 31 2009 - 09:38:18 CDT)
- Re: [AMBER] problem from xleap Tom Joseph (Fri Jul 31 2009 - 11:41:49 CDT)
  - Re: [AMBER] problem from xleap Qinghua Liao (Fri Jul 31 2009 - 20:38:19 CDT)
    - Re: [AMBER] problem from xleap Ashish Runthala (Fri Jul 31 2009 - 22:33:10 CDT)
    - Re: [AMBER] problem from xleap Tom Joseph (Sat Aug 01 2009 - 06:19:22 CDT)
[AMBER] Protonated or not s. Bill (Fri Jul 31 2009 - 12:15:32 CDT)
- Re: [AMBER] Protonated or not Adrian Roitberg (Fri Jul 31 2009 - 12:32:50 CDT)
  - [AMBER] Protein Activity Chih-Ying Lin (Tue Aug 04 2009 - 12:57:54 CDT)
  - [AMBER] Protein Domain Motion Chih-Ying Lin (Thu Aug 13 2009 - 14:20:09 CDT)
[AMBER] Metalloproteins - Ligand Protonation s. Bill (Fri Jul 31 2009 - 13:01:42 CDT)
[AMBER] radial distribution function Dharmik Meghana shankar (Sat Aug 01 2009 - 00:33:58 CDT)
[AMBER] Timescales and restraints for protein-small ligands movement simulations Andrew Voronkov (Sat Aug 01 2009 - 01:23:19 CDT)
- Re: [AMBER] Timescales and restraints for protein-small ligands movement simulations Andrew Voronkov (Sat Aug 01 2009 - 09:14:49 CDT)
  - Re: [AMBER] Timescales and restraints for protein-small ligands movement simulations Vivek Sharma (Sun Aug 02 2009 - 01:29:13 CDT)
[AMBER] Showing error bharat lakhani (Sat Aug 01 2009 - 08:12:00 CDT)
[AMBER] Showing error in energy minimization bharat lakhani (Sun Aug 02 2009 - 01:22:30 CDT)
- Re: [AMBER] Showing error in energy minimization case (Sun Aug 02 2009 - 09:25:04 CDT)
  - [AMBER] Do we need to need to rms fit all atoms before calculating correlation motion between residues? Catein Catherine (Sun Aug 02 2009 - 22:45:19 CDT)
- Re: [AMBER] Showing error in energy minimization Ashish Runthala (Sun Aug 02 2009 - 22:05:06 CDT)
[AMBER] showing error when creating topology and coordinate file bharat lakhani (Mon Aug 03 2009 - 02:19:59 CDT)
- [AMBER] Re: showing error when creating topology and coordinate file bharat lakhani (Mon Aug 03 2009 - 23:54:36 CDT)
  - RE: [AMBER] Re: showing error when creating topology and coordinate file Olotu Odunayo (Tue Aug 04 2009 - 08:08:32 CDT)
[AMBER] optimization step length ondrej.prenosil_at_marge.uochb.cas.cz (Mon Aug 03 2009 - 05:40:15 CDT)
- Re: [AMBER] optimization step length Ashish Runthala (Mon Aug 03 2009 - 09:26:28 CDT)
[AMBER] Problem with Amber8 Sebastian Petruczynik (Mon Aug 03 2009 - 08:28:56 CDT)
- Re: [AMBER] Problem with Amber8 ondrej.prenosil_at_marge.uochb.cas.cz (Mon Aug 03 2009 - 08:37:01 CDT)
- RE: [AMBER] Problem with Amber8 Ross Walker (Mon Aug 03 2009 - 14:41:28 CDT)
  - Re: [AMBER] Problem with Amber8 Sebastian Petruczynik (Wed Aug 05 2009 - 06:33:05 CDT)
[AMBER] What is the meaning of IED values for PCA analysis? Catein Catherine (Mon Aug 03 2009 - 09:30:15 CDT)
- Re: [AMBER] What is the meaning of IED values for PCA analysis? case (Wed Aug 05 2009 - 11:39:30 CDT)
[AMBER] How to solve the problem "RESTARTED DUE to LINMIN FAILURE" Jianping Lin (Mon Aug 03 2009 - 09:57:28 CDT)
- RE: [AMBER] How to solve the problem "RESTARTED DUE to LINMIN FAILURE" Ross Walker (Mon Aug 03 2009 - 14:38:23 CDT)
  - Re: [AMBER] How to solve the problem "RESTARTED DUE to LINMIN FAILURE" Jianping Lin (Fri Aug 07 2009 - 15:32:47 CDT)
- [AMBER] Re: How to solve the problem "RESTARTED DUE to LINMIN FAILURE" Jianping Lin (Mon Aug 10 2009 - 18:18:44 CDT)
  - Re: [AMBER] Re: How to solve the problem "RESTARTED DUE to LINMIN FAILURE" Bill Ross (Mon Aug 10 2009 - 20:17:05 CDT)
    - Re: [AMBER] Re: How to solve the problem "RESTARTED DUE to LINMIN FAILURE" Jianping Lin (Mon Aug 10 2009 - 20:23:44 CDT)
  - Re: [AMBER] Re: How to solve the problem "RESTARTED DUE to LINMIN FAILURE" Bill Ross (Mon Aug 10 2009 - 20:30:07 CDT)
[AMBER] Lennard Jones potential Rizwan Tai (Mon Aug 03 2009 - 12:13:16 CDT)
- RE: [AMBER] Lennard Jones potential Ross Walker (Mon Aug 03 2009 - 14:28:06 CDT)
[AMBER] parmchk problem isaac sugden (Tue Aug 04 2009 - 09:12:29 CDT)
- Re: [AMBER] parmchk problem case (Wed Aug 05 2009 - 11:36:27 CDT)
  - Re: [AMBER] parmchk problem isaac sugden (Wed Aug 05 2009 - 12:21:53 CDT)
    - Re: [AMBER] parmchk problem case (Tue Aug 11 2009 - 08:51:57 CDT)
Re: [AMBER] Protein Activity Bill Ross (Tue Aug 04 2009 - 14:19:32 CDT)
- Re: [AMBER] Protein Activity Chih-Ying Lin (Tue Aug 04 2009 - 14:42:42 CDT)
- Re: [AMBER] Protein Activity Bill Ross (Tue Aug 04 2009 - 14:59:40 CDT)
  - Re: [AMBER] Protein Activity Ashish Runthala (Tue Aug 04 2009 - 22:42:11 CDT)
[AMBER] problem of mm_pbsa Qinghua Liao (Wed Aug 05 2009 - 00:46:51 CDT)
- Re: [AMBER] problem of mm_pbsa case (Wed Aug 05 2009 - 10:42:56 CDT)
  - Re: [AMBER] problem of mm_pbsa Qinghua Liao (Wed Aug 05 2009 - 19:22:13 CDT)
  - Re: [AMBER] problem of mm_pbsa Rubben Torella (Thu Aug 06 2009 - 10:53:47 CDT)
[AMBER] USE A VERSION COMPILED WITHOUT -DLES s. Bill (Wed Aug 05 2009 - 05:50:01 CDT)
- Solved THNAKS Re: [AMBER] USE A VERSION COMPILED WITHOUT -DLES s. Bill (Wed Aug 05 2009 - 06:55:55 CDT)
[AMBER] TWO restraints with different force constants s. Bill (Wed Aug 05 2009 - 06:54:18 CDT)
- Re: [AMBER] TWO restraints with different force constants A. Gomez-Sicilia (Wed Aug 05 2009 - 07:20:54 CDT)
AW: [AMBER] TWO restraints with different force constants Aust, Susanne (Wed Aug 05 2009 - 07:31:38 CDT)
[AMBER] Computational Resources s. Bill (Wed Aug 05 2009 - 10:17:34 CDT)
- RE: [AMBER] Computational Resources Ross Walker (Wed Aug 05 2009 - 11:08:21 CDT)
[AMBER] ptraj failure to parse psf input Sasha Buzko (Wed Aug 05 2009 - 11:39:57 CDT)
- Re: [AMBER] ptraj failure to parse psf input case (Wed Aug 05 2009 - 12:32:00 CDT)
  - Re: [AMBER] ptraj failure to parse psf input Sasha Buzko (Wed Aug 05 2009 - 14:33:54 CDT)
- Re: [AMBER] ptraj failure to parse psf input Sasha Buzko (Wed Aug 12 2009 - 16:16:07 CDT)
- Re: [AMBER] ptraj failure to parse psf input Thomas Cheatham (Wed Aug 12 2009 - 23:27:34 CDT)
  - Re: [AMBER] ptraj failure to parse psf input Sasha Buzko (Thu Aug 13 2009 - 11:25:32 CDT)
- Re: [AMBER] ptraj failure to parse psf input Sasha Buzko (Thu Aug 13 2009 - 18:34:07 CDT)
[AMBER] nmode output Vahdati N. (Wed Aug 05 2009 - 17:26:11 CDT)
[AMBER] implicit solvent simulation Manish Kumar (Wed Aug 05 2009 - 23:49:30 CDT)
- Re: [AMBER] implicit solvent simulation Ashish Runthala (Thu Aug 06 2009 - 00:00:50 CDT)
  - Re: [AMBER] implicit solvent simulation Manish Kumar (Thu Aug 06 2009 - 00:19:11 CDT)
- RE: [AMBER] implicit solvent simulation Ross Walker (Thu Aug 06 2009 - 01:32:24 CDT)
  - Re: [AMBER] implicit solvent simulation Manish Kumar (Thu Aug 06 2009 - 01:53:54 CDT)
[AMBER] Model(l)ing'09 in Erlangen, Germany: Registration Open Until August 31st Harald Lanig (Thu Aug 06 2009 - 03:39:07 CDT)
[AMBER] Extreme optimization problems ondrej.prenosil_at_marge.uochb.cas.cz (Thu Aug 06 2009 - 07:04:09 CDT)
- Re: [AMBER] Extreme optimization problems case (Thu Aug 06 2009 - 10:51:23 CDT)
[AMBER] parameters for HIV protease inhibitors Oliver Kuhn (Thu Aug 06 2009 - 09:51:03 CDT)
- Re: [AMBER] parameters for HIV protease inhibitors Carlos Simmerling (Thu Aug 06 2009 - 10:29:39 CDT)
- Re: [AMBER] parameters for HIV protease inhibitors Oliver Kuhn (Tue Aug 11 2009 - 09:57:24 CDT)
- Re: [AMBER] parameters for HIV protease inhibitors FyD (Wed Aug 12 2009 - 07:56:18 CDT)
[AMBER] Regd : gaff force field KIRTANA S (Thu Aug 06 2009 - 15:09:14 CDT)
- Re: [AMBER] Regd : gaff force field Nicholas Musolino (Thu Aug 06 2009 - 15:22:37 CDT)
- RE: [AMBER] Regd : gaff force field Ross Walker (Thu Aug 06 2009 - 15:42:14 CDT)
  - Re: [AMBER] Regd : gaff force field KIRTANA S (Thu Aug 06 2009 - 17:12:15 CDT)
[AMBER] How to keep the closest solvent mols to each atoms by PTRAJ? u8613020_at_msg.ndhu.edu.tw (Thu Aug 06 2009 - 20:40:17 CDT)
[AMBER] implicit solvent simulation with new ligand Manish Kumar (Thu Aug 06 2009 - 22:29:37 CDT)
- [AMBER] Re: implicit solvent simulation with new ligand Manish Kumar (Fri Aug 07 2009 - 13:22:57 CDT)
  - Re: [AMBER] Re: implicit solvent simulation with new ligand Carlos Simmerling (Fri Aug 07 2009 - 13:29:46 CDT)
[AMBER] query bharat lakhani (Fri Aug 07 2009 - 04:11:42 CDT)
- Re: [AMBER] query Pansy Patel (Fri Jul 31 2009 - 09:41:05 CDT)
  - Re: [AMBER] query Ashish Runthala (Fri Jul 31 2009 - 20:23:07 CDT)
[AMBER] pmemd michael (Fri Aug 07 2009 - 04:50:29 CDT)
- Re: [AMBER] pmemd case (Fri Aug 07 2009 - 10:18:52 CDT)
  - Re: [AMBER] pmemd michael (Mon Aug 10 2009 - 14:51:59 CDT)
[AMBER] query regarding resp subarna thakur (Fri Aug 07 2009 - 07:14:35 CDT)
- Re: [AMBER] query regarding resp Oliver Kuhn (Tue Aug 11 2009 - 09:24:19 CDT)
[AMBER] (no subject) Beale, John (Fri Aug 07 2009 - 07:16:58 CDT)
- Re: [AMBER] (no subject) Ashish Runthala (Fri Aug 07 2009 - 08:27:04 CDT)
- RE: [AMBER] (no subject) Ross Walker (Fri Aug 07 2009 - 10:35:32 CDT)
  - Re: [AMBER] (no subject) case (Fri Aug 07 2009 - 18:54:18 CDT)
[AMBER] MM-PBSA results Dmitry Osolodkin (Fri Aug 07 2009 - 09:31:48 CDT)
[AMBER] Appropriate nmode input file for gas and vacuum phase simulation Scott Pendley (Fri Aug 07 2009 - 12:48:52 CDT)
[AMBER] antechamber am1-bcc issues David Mobley (Fri Aug 07 2009 - 13:19:53 CDT)
- [AMBER] Re: antechamber am1-bcc issues case (Fri Aug 07 2009 - 18:54:38 CDT)
  - Re: [AMBER] Re: antechamber am1-bcc issues gilbert_at_bluemarble.net (Sat Aug 08 2009 - 08:55:40 CDT)
    - Re: [AMBER] Re: antechamber am1-bcc issues case (Sat Aug 08 2009 - 14:20:44 CDT)
    - Re: [AMBER] Re: antechamber am1-bcc issues David Mobley (Thu Aug 13 2009 - 08:25:52 CDT)
  - Re: [AMBER] Re: antechamber am1-bcc issues Khavrutskii, Ilja (Fri Aug 21 2009 - 11:27:28 CDT)
    - Re: [AMBER] Re: antechamber am1-bcc issues Khavrutskii, Ilja (Fri Aug 21 2009 - 14:32:34 CDT)
- Re: [AMBER] antechamber am1-bcc issues Khavrutskii, Ilja (Tue Aug 18 2009 - 16:00:03 CDT)
  - Re: [AMBER] antechamber am1-bcc issues Alan (Thu Aug 20 2009 - 03:28:09 CDT)
- Re: [AMBER] antechamber am1-bcc issues case (Thu Aug 20 2009 - 06:18:52 CDT)
[AMBER] Error in equilibration: file _ew_box.f Biswaranjan Meher (Fri Aug 07 2009 - 15:39:00 CDT)
- Re: [AMBER] Error in equilibration: file _ew_box.f case (Fri Aug 07 2009 - 17:34:29 CDT)
[AMBER] Why..QM/MM s. Bill (Sat Aug 08 2009 - 06:26:46 CDT)
- RE: [AMBER] Why..QM/MM Ross Walker (Sat Aug 08 2009 - 12:00:27 CDT)
[AMBER] hydrogen bond? Jio M (Sun Aug 09 2009 - 06:29:23 CDT)
[AMBER] Regarding Minimization maxcyc Ashish Runthala (Sun Aug 09 2009 - 09:09:58 CDT)
- Re: [AMBER] Regarding Minimization maxcyc case (Mon Aug 10 2009 - 09:43:00 CDT)
[AMBER] DivCon - QM/MM s. Bill (Mon Aug 10 2009 - 09:11:39 CDT)
- Solved thanks Re: [AMBER] DivCon - QM/MM s. Bill (Tue Aug 11 2009 - 02:54:38 CDT)
[AMBER] Any Comment, please s. Bill (Tue Aug 11 2009 - 02:56:20 CDT)
AW: [AMBER] Any Comment, please Aust, Susanne (Tue Aug 11 2009 - 03:17:18 CDT)
- Re: AW: [AMBER] Any Comment, please s. Bill (Tue Aug 11 2009 - 03:22:16 CDT)
AW: AW: [AMBER] Any Comment, please Aust, Susanne (Tue Aug 11 2009 - 03:36:34 CDT)
- [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? Catein Catherine (Tue Aug 11 2009 - 06:10:09 CDT)
  - Re: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? case (Tue Aug 11 2009 - 06:54:43 CDT)
[AMBER] Amber99SB eric johnson (Tue Aug 11 2009 - 09:33:34 CDT)
- Re: [AMBER] Amber99SB Carlos Simmerling (Tue Aug 11 2009 - 09:42:44 CDT)
[AMBER] suggestions pls Jio M (Tue Aug 11 2009 - 12:44:19 CDT)
- [AMBER] measuring volume of the binding pocket Mannan (Tue Aug 11 2009 - 21:03:49 CDT)
  - [AMBER] Measuring volume of the binding pocket Mannan (Tue Aug 11 2009 - 21:31:18 CDT)
- Re: [AMBER] suggestions pls Ashish Runthala (Tue Aug 11 2009 - 21:40:40 CDT)
  - Re: [AMBER] suggestions pls Jio M (Wed Aug 12 2009 - 08:04:16 CDT)
[AMBER] query regarding fes cluster subarna thakur (Wed Aug 12 2009 - 00:39:55 CDT)
- Re: [AMBER] query regarding fes cluster FyD (Wed Aug 12 2009 - 08:00:37 CDT)
[AMBER] gaussian 98 input/output for antechamber/resp wong105_at_llnl.gov (Wed Aug 12 2009 - 13:41:45 CDT)
- Re: [AMBER] gaussian 98 input/output for antechamber/resp Karl Kirschner (Thu Aug 13 2009 - 01:57:41 CDT)
- Re: [AMBER] gaussian 98 input/output for antechamber/resp Karl Kirschner (Thu Aug 13 2009 - 02:26:12 CDT)
[AMBER] REMD using hybrid solvent model Morad Mustafa (Wed Aug 12 2009 - 14:05:40 CDT)
[AMBER] CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS FULL PDB Manish Kumar (Wed Aug 12 2009 - 14:44:37 CDT)
- Re: [AMBER] CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS FULL PDB case (Wed Aug 12 2009 - 14:57:33 CDT)
  - Re: [AMBER] CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS FULL PDB Hector A. Baldoni (Wed Aug 12 2009 - 15:43:28 CDT)
[Amber]: REMD using hybrid solvent model Morad Mustafa (Wed Aug 12 2009 - 16:30:01 CDT)
- Re: [Amber]: REMD using hybrid solvent model Carlos Simmerling (Wed Aug 12 2009 - 18:52:56 CDT)
  - Re: [Amber]: REMD using hybrid solvent model Morad Mustafa (Fri Aug 14 2009 - 07:44:44 CDT)
    - [AMBER] Gaussian network model (GNM) Chih-Ying Lin (Fri Aug 21 2009 - 19:39:07 CDT)
    - Re: [AMBER] Gaussian network model (GNM) Adrian Roitberg (Fri Aug 21 2009 - 19:49:04 CDT)
- Re: [Amber]: REMD using hybrid solvent model Carlos Simmerling (Wed Aug 12 2009 - 18:54:20 CDT)
[AMBER] sourcing leap commands in log file Donald Keidel (Wed Aug 12 2009 - 19:32:31 CDT)
Re: [AMBER] sourcing leap commands in log file Bill Ross (Wed Aug 12 2009 - 19:47:57 CDT)
- Re: [AMBER] sourcing leap commands in log file Ashish Runthala (Sat Aug 15 2009 - 01:50:31 CDT)
[AMBER] reset velocity Parimal Kar (Wed Aug 12 2009 - 20:01:33 CDT)
- Re: [AMBER] reset velocity Tom Joseph (Thu Aug 13 2009 - 01:26:48 CDT)
[AMBER] ptraj imaging of namd generated trajectories Vlad Cojocaru (Thu Aug 13 2009 - 04:35:49 CDT)
- [AMBER] Re: ptraj imaging of namd generated trajectories Vlad Cojocaru (Thu Aug 13 2009 - 05:10:54 CDT)
[AMBER] ptraj-image Nancy (Thu Aug 13 2009 - 05:35:01 CDT)
[AMBER] box problem Nancy (Thu Aug 13 2009 - 06:20:20 CDT)
- Re: [AMBER] box problem case (Thu Aug 13 2009 - 06:50:54 CDT)
  - Re:Re: [AMBER] box problem Nancy (Thu Aug 13 2009 - 21:43:02 CDT)
  - Re:Re: [AMBER] box problem Nancy (Mon Aug 17 2009 - 21:49:20 CDT)
[AMBER] NAB optimization ondrej.prenosil_at_marge.uochb.cas.cz (Thu Aug 13 2009 - 08:45:26 CDT)
- Re: [AMBER] NAB optimization case (Thu Aug 13 2009 - 08:56:28 CDT)
[AMBER] drying of solvent possible ? Jio M (Thu Aug 13 2009 - 08:49:00 CDT)
[AMBER] Strange QM/MM Divcon - help me out s. Bill (Thu Aug 13 2009 - 10:37:54 CDT)
- Re: [AMBER] Strange QM/MM Divcon - help me out case (Thu Aug 13 2009 - 10:52:34 CDT)
  - Re: [AMBER] Strange QM/MM Divcon - help me out Ashish Runthala (Sat Aug 15 2009 - 01:42:38 CDT)
    - RE: [AMBER] Strange QM/MM Divcon - help me out Ross Walker (Sun Aug 16 2009 - 11:55:01 CDT)
[AMBER] QM/MM types. ros_at_servidor.unam.mx (Thu Aug 13 2009 - 10:49:02 CDT)
- RE: [AMBER] QM/MM types. Ross Walker (Thu Aug 13 2009 - 11:11:57 CDT)
Re: [AMBER] drying of solvent possible ? Bill Ross (Thu Aug 13 2009 - 11:21:35 CDT)
- Re: [AMBER] drying of solvent possible ? Jio M (Sat Aug 15 2009 - 00:59:08 CDT)
[AMBER] Charge Problem s. Bill (Fri Aug 14 2009 - 03:25:05 CDT)
- Re: [AMBER] Charge Problem Karl Kirschner (Fri Aug 14 2009 - 03:55:07 CDT)
- Re: [AMBER] Charge Problem FyD (Sat Aug 15 2009 - 07:06:45 CDT)
[AMBER] MM_PBSA not successful workalemahu berhanu (Fri Aug 14 2009 - 16:45:41 CDT)
- Re: [AMBER] MM_PBSA not successful Jordan Monnet (Fri Aug 14 2009 - 19:05:00 CDT)
  - Re: [AMBER] MM_PBSA not successful workalemahu berhanu (Fri Aug 14 2009 - 21:21:32 CDT)
- Re: [AMBER] MM_PBSA not successful Qinghua Liao (Fri Aug 14 2009 - 20:20:55 CDT)
  - Re: [AMBER] MM_PBSA not successful workalemahu berhanu (Fri Aug 14 2009 - 21:36:39 CDT)
- Re: [AMBER] MM_PBSA not successful monnet.jordan_at_free.fr (Sat Aug 15 2009 - 17:10:08 CDT)
  - Re: [AMBER] MM_PBSA not successful workalemahu berhanu (Sun Aug 16 2009 - 12:22:01 CDT)
    - RE: [AMBER] MM_PBSA not successful Ross Walker (Sun Aug 16 2009 - 13:15:42 CDT)
[AMBER] AMBER job restart problem Kefa Lu (Sat Aug 15 2009 - 03:22:08 CDT)
- Re: [AMBER] AMBER job restart problem Ashish Runthala (Sat Aug 15 2009 - 04:57:48 CDT)
  - Re: [AMBER] AMBER job restart problem Kefa Lu (Sat Aug 15 2009 - 05:12:21 CDT)
- Re: [AMBER] AMBER job restart problem case (Sat Aug 15 2009 - 08:49:44 CDT)
  - Re: [AMBER] AMBER job restart problem Ashish Runthala (Sat Aug 15 2009 - 09:39:56 CDT)
    - Re: [AMBER] AMBER job restart problem case (Sat Aug 15 2009 - 10:40:51 CDT)
- Re: [AMBER] AMBER job restart problem Thomas Cheatham (Sat Aug 15 2009 - 10:49:10 CDT)
  - Re: [AMBER] AMBER job restart problem Kefa Lu (Sat Aug 15 2009 - 23:36:59 CDT)
    - Re: [AMBER] AMBER job restart problem Thomas Cheatham (Sat Aug 15 2009 - 23:44:27 CDT)
    - Re: [AMBER] AMBER job restart problem Kefa Lu (Sun Aug 16 2009 - 00:09:22 CDT)
[AMBER] AMBER on a Mac Mini cluster PoC Abdul Rehman Gani (Sun Aug 16 2009 - 10:51:44 CDT)
- RE: [AMBER] AMBER on a Mac Mini cluster PoC Ross Walker (Sun Aug 16 2009 - 12:08:47 CDT)
  - Re: [AMBER] AMBER on a Mac Mini cluster PoC Abdul Rehman Gani (Mon Aug 17 2009 - 03:13:38 CDT)
[AMBER] Variations of the number of total hydrogen bond in MD simulations using ptraj workalemahu berhanu (Sun Aug 16 2009 - 15:13:21 CDT)
[AMBER] gaussain output subarna thakur (Mon Aug 17 2009 - 02:11:00 CDT)
- Re: [AMBER] gaussain output FyD (Mon Aug 17 2009 - 04:50:53 CDT)
  - Re: [AMBER] gaussain output FyD (Mon Aug 17 2009 - 17:59:39 CDT)
[AMBER] [AmberTool] xleap problem ÁÖÅÂ¼º (Mon Aug 17 2009 - 03:57:37 CDT)
[AMBER] amber 10 test fails with pathscale 3.2 Raj (Mon Aug 17 2009 - 07:54:45 CDT)
- RE: [AMBER] amber 10 test fails with pathscale 3.2 Ross Walker (Mon Aug 17 2009 - 11:34:28 CDT)
Re: [AMBER] Variations of the number of total hydrogen bond in MD simulations using ptraj workalemahu berhanu (Mon Aug 17 2009 - 08:26:35 CDT)
- Re: [AMBER] Variations of the number of total hydrogen bond in MD simulations using ptraj Paul Frybarger (Mon Aug 17 2009 - 12:57:28 CDT)
[AMBER] amber test fails with ICC 11.0.081 Raj (Mon Aug 17 2009 - 09:57:57 CDT)
- Re: [AMBER] amber test fails with ICC 11.0.081 Carlos Simmerling (Mon Aug 17 2009 - 10:16:26 CDT)
[AMBER] Can i link and refine two domains of a single protein Ashish Runthala (Mon Aug 17 2009 - 10:32:33 CDT)
[AMBER] Re: [q4md-fft] charge calculation FyD (Mon Aug 17 2009 - 18:40:49 CDT)
[AMBER] AMBER is running silently Kefa Lu (Mon Aug 17 2009 - 17:47:34 CDT)
Re: [AMBER] AMBER is running silently Bill Ross (Mon Aug 17 2009 - 18:04:02 CDT)
- Re: [AMBER] AMBER is running silently Kefa Lu (Mon Aug 17 2009 - 18:10:17 CDT)
  - RE: [AMBER] AMBER is running silently Ross Walker (Mon Aug 17 2009 - 18:33:09 CDT)
    - Re: [AMBER] AMBER is running silently Kefa Lu (Mon Aug 17 2009 - 20:25:14 CDT)
[AMBER] antechamber execution subarna thakur (Tue Aug 18 2009 - 01:06:52 CDT)
- Re: [AMBER] antechamber execution FyD (Tue Aug 18 2009 - 18:59:40 CDT)
[AMBER] Can i link and refine the modeled domains with different proteins bound on it Ashish Runthala (Tue Aug 18 2009 - 06:13:23 CDT)
[AMBER] RDC import from PALES Thomas Pochapsky (Tue Aug 18 2009 - 09:33:42 CDT)
- Re: [AMBER] RDC import from PALES case (Fri Aug 28 2009 - 07:01:30 CDT)
[AMBER] Dimethyl Sulfoxide (DMSO) cartesian coordinates? Jose Borreguero (Tue Aug 18 2009 - 09:37:39 CDT)
- Re: [AMBER] Dimethyl Sulfoxide (DMSO) cartesian coordinates? FyD (Tue Aug 18 2009 - 19:05:19 CDT)
  - Re: [AMBER] Dimethyl Sulfoxide (DMSO) cartesian coordinates? Jose Borreguero (Tue Aug 18 2009 - 17:33:32 CDT)
- Re: [AMBER] Dimethyl Sulfoxide (DMSO) cartesian coordinates? Bill Ross (Tue Aug 18 2009 - 17:59:12 CDT)
[AMBER] ***PROBLEMS WITH GROUPLRES Maria Mirza (Tue Aug 18 2009 - 19:34:41 CDT)
[AMBER] Distance restraint and periodic boundary conditions Cyril Falvo (Tue Aug 18 2009 - 19:58:29 CDT)
- Re: [AMBER] Distance restraint and periodic boundary conditions Thomas Cheatham (Tue Aug 18 2009 - 20:23:56 CDT)
- Re: [AMBER] Distance restraint and periodic boundary conditions case (Tue Aug 18 2009 - 21:02:45 CDT)
  - Re: [AMBER] Distance restraint and periodic boundary conditions Peter Varnai (Wed Aug 19 2009 - 10:13:04 CDT)
[AMBER] RESP charges of Fe4S4 cluster subarna thakur (Wed Aug 19 2009 - 02:53:20 CDT)
- Re: [AMBER] RESP charges of Fe4S4 cluster vhakkim boy (Wed Aug 19 2009 - 03:40:59 CDT)
- Re: [AMBER] RESP charges of Fe4S4 cluster case (Fri Aug 21 2009 - 09:13:23 CDT)
AW: [AMBER] Conference or workshop on AMBER? Aust, Susanne (Wed Aug 19 2009 - 03:16:21 CDT)
[AMBER] resp calculation for rubredoxin vhakkim boy (Wed Aug 19 2009 - 05:11:22 CDT)
[AMBER] Problem with loading PDB into tleap Kamali Sripathi (Wed Aug 19 2009 - 08:21:30 CDT)
- Re: [AMBER] Problem with loading PDB into tleap Ashish Runthala (Wed Aug 19 2009 - 08:56:59 CDT)
  - Re: [AMBER] Problem with loading PDB into tleap Kamali Sripathi (Wed Aug 19 2009 - 09:06:15 CDT)
- Re: [AMBER] Problem with loading PDB into tleap case (Wed Aug 19 2009 - 18:55:52 CDT)
  - Re: [AMBER] Problem with loading PDB into tleap Ashish Runthala (Wed Aug 19 2009 - 21:53:04 CDT)
    - Re: [AMBER] Problem with loading PDB into tleap Kamali Sripathi (Tue Sep 08 2009 - 08:49:20 CDT)
    - Re: [AMBER] Problem with loading PDB into tleap Ashish Runthala (Tue Sep 08 2009 - 10:14:46 CDT)
[AMBER] why is nonpolar solvation energy not implemented for dynamic in amber TaoPaul (Wed Aug 19 2009 - 10:29:38 CDT)
[AMBER] ptraj cluster - snapshot number of a representative structure Marcin Krol (Thu Aug 20 2009 - 03:26:09 CDT)
- Re: [AMBER] ptraj cluster - snapshot number of a representative structure Jianyin Shao (Thu Aug 20 2009 - 10:50:22 CDT)
[AMBER] box volume not understood? Jio M (Thu Aug 20 2009 - 08:54:52 CDT)
- RE: [AMBER] box volume not understood? Ross Walker (Thu Aug 20 2009 - 10:43:42 CDT)
  - RE: [AMBER] box volume not understood? Jio M (Thu Aug 20 2009 - 13:26:41 CDT)
    - RE: [AMBER] box volume not understood? Ross Walker (Thu Aug 20 2009 - 18:21:00 CDT)
    - RE: [AMBER] box volume not understood? Jio M (Thu Aug 20 2009 - 23:43:31 CDT)
- RE: [AMBER] box volume not understood? Bill Ross (Thu Aug 20 2009 - 21:53:52 CDT)
- RE: [AMBER] box volume not understood? Bill Ross (Fri Aug 21 2009 - 11:15:51 CDT)
[AMBER] center of mass dhacademic (Thu Aug 20 2009 - 15:50:47 CDT)
[AMBER] mm_pbsa-Binding and Stability tests? Antonija TomiÄ‡ (Fri Aug 21 2009 - 05:04:35 CDT)
- RE: [AMBER] mm_pbsa-Binding and Stability tests? Niel Henriksen (Fri Aug 21 2009 - 09:52:49 CDT)
  - RE: [AMBER] mm_pbsa-Binding and Stability tests? Antonija TomiÄ‡ (Mon Aug 24 2009 - 04:51:28 CDT)
    - RE: [AMBER] mm_pbsa-Binding and Stability tests? Niel Henriksen (Mon Aug 24 2009 - 12:24:09 CDT)
    - RE: [AMBER] mm_pbsa-Binding and Stability tests? Antonija TomiÄ‡ (Wed Aug 26 2009 - 04:15:54 CDT)
- Re: [AMBER] mm_pbsa-Binding and Stability tests? Ray Luo (Fri Aug 21 2009 - 16:29:58 CDT)
[AMBER] update on am1-bcc charge problem in antechamber case (Fri Aug 21 2009 - 11:32:30 CDT)
[AMBER] PMEMD 10 overflow issues ben rodriguez (Fri Aug 21 2009 - 15:38:05 CDT)
- RE: [AMBER] PMEMD 10 overflow issues Ross Walker (Fri Aug 21 2009 - 15:57:12 CDT)
  - RE: [AMBER] PMEMD 10 overflow issues ben rodriguez (Fri Aug 21 2009 - 16:17:36 CDT)
[AMBER] protein-ligand binding simulation times Andrew Voronkov (Sat Aug 22 2009 - 00:09:54 CDT)
- Re: [AMBER] protein-ligand binding simulation times steinbrt_at_rci.rutgers.edu (Sat Aug 22 2009 - 04:50:35 CDT)
  - Re: [AMBER] protein-ligand binding simulation times Andrew Voronkov (Sat Aug 22 2009 - 05:32:42 CDT)
[AMBER] ambpdb water removal for rst files Andrew Voronkov (Sat Aug 22 2009 - 01:53:14 CDT)
- Re: [AMBER] ambpdb water removal for rst files Andrew Voronkov (Sun Dec 06 2009 - 13:44:28 CST)
- Re: [AMBER] ambpdb water removal for rst files Bill Ross (Sun Dec 06 2009 - 14:03:00 CST)
- Re: [AMBER] ambpdb water removal for rst files Bill Ross (Sun Dec 06 2009 - 14:09:26 CST)
Re: [AMBER] ambpdb water removal for rst files Bill Ross (Sat Aug 22 2009 - 09:45:30 CDT)
[AMBER] ptraj-rms vs carnal; questions on RMSD of ligand drift Andrew Voronkov (Sun Aug 23 2009 - 06:55:01 CDT)
[AMBER] Re: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) Andrew Voronkov (Sun Aug 23 2009 - 08:48:07 CDT)
[AMBER] acetone lib and frcmod files? Jose Borreguero (Sun Aug 23 2009 - 16:36:43 CDT)
- RE: [AMBER] acetone lib and frcmod files? Ross Walker (Mon Aug 24 2009 - 00:08:16 CDT)
  - RE: [AMBER] acetone lib and frcmod files? FyD (Mon Aug 24 2009 - 02:31:40 CDT)
[AMBER] ABMD Reaction Coordinates stephane acoca (Sun Aug 23 2009 - 22:11:09 CDT)
[AMBER] ABMD Reaction Coordinates stephane acoca (Sun Aug 23 2009 - 22:24:32 CDT)
[AMBER] ABMD Reaction Coordinates stephane acoca (Sun Aug 23 2009 - 22:25:43 CDT)
[AMBER] ABMD Reaction Coordinates stephane acoca (Mon Aug 24 2009 - 00:04:58 CDT)
[AMBER] Note regarding posting of the same message multiple times Ross Walker (Mon Aug 24 2009 - 00:19:36 CDT)
[AMBER] Meaning of GMAX E.M. (Mon Aug 24 2009 - 04:05:10 CDT)
- Re: [AMBER] Meaning of GMAX case (Mon Aug 24 2009 - 06:44:34 CDT)
  - Re: [AMBER] Meaning of GMAX Ashish Runthala (Mon Aug 24 2009 - 09:59:53 CDT)
    - Re: [AMBER] Meaning of GMAX Adrian Roitberg (Mon Aug 24 2009 - 10:05:36 CDT)
    - Re: [AMBER] Meaning of GMAX Ashish Runthala (Mon Aug 24 2009 - 10:38:46 CDT)
[AMBER] how to add a new atomtype for MM/GB/SA decomposition analysis TaoPaul (Mon Aug 24 2009 - 09:03:51 CDT)
[AMBER] ptraj limit on trajectory size Sasha Buzko (Mon Aug 24 2009 - 11:59:30 CDT)
- RE: [AMBER] ptraj limit on trajectory size Ross Walker (Mon Aug 24 2009 - 17:07:00 CDT)
  - Re: [AMBER] ptraj limit on trajectory size Sasha Buzko (Mon Aug 24 2009 - 17:31:14 CDT)
[AMBER] problem compiling amber tools with gcc-4.4.1 gilbert_at_bluemarble.net (Mon Aug 24 2009 - 22:07:44 CDT)
- Re: [AMBER] problem compiling amber tools with gcc-4.4.1 case (Tue Aug 25 2009 - 07:52:35 CDT)
[AMBER] sander does not print out all residues in range. Maria Mirza (Mon Aug 24 2009 - 23:32:31 CDT)
- RE: [AMBER] sander does not print out all residues in range. Ross Walker (Tue Aug 25 2009 - 00:00:03 CDT)
  - Re: [AMBER] sander does not print out all residues in range. Maria Mirza (Tue Aug 25 2009 - 00:17:59 CDT)
[AMBER] NATOM in prmtop and inpcrd files does not agree with the input Maria Mirza (Mon Aug 24 2009 - 23:41:39 CDT)
- RE: [AMBER] NATOM in prmtop and inpcrd files does not agree with the input Ross Walker (Mon Aug 24 2009 - 23:55:52 CDT)
  - Re: [AMBER] NATOM in prmtop and inpcrd files does not agree with the input Ashish Runthala (Tue Aug 25 2009 - 00:45:33 CDT)
    - RE: [AMBER] NATOM in prmtop and inpcrd files does not agree with the input Ross Walker (Tue Aug 25 2009 - 12:55:39 CDT)
[AMBER] ambertools test faied subarna thakur (Tue Aug 25 2009 - 06:01:12 CDT)
- Re: [AMBER] ambertools test faied case (Tue Aug 25 2009 - 06:39:16 CDT)
[AMBER] Epsilon value for Iron bharat lakhani (Tue Aug 25 2009 - 07:24:10 CDT)
- [AMBER] how much % of the total protein motion are described by the first eigenvector? Catein Catherine (Wed Aug 26 2009 - 04:05:17 CDT)
  - Re: [AMBER] how much % of the total protein motion are described by the first eigenvector? Hannes Loeffler (Wed Aug 26 2009 - 04:41:31 CDT)
[AMBER] Single Adenine ros (Wed Aug 26 2009 - 01:09:23 CDT)
- Re: [AMBER] Single Adenine case (Wed Aug 26 2009 - 06:36:09 CDT)
  - Re: [AMBER] Single Adenine case (Wed Aug 26 2009 - 06:48:36 CDT)
- Re: [AMBER] Single Adenine Bill Ross (Wed Aug 26 2009 - 14:28:31 CDT)
[AMBER] Chirality error in pdb xiawei (Wed Aug 26 2009 - 02:02:43 CDT)
- Re: [AMBER] Chirality error in pdb case (Wed Aug 26 2009 - 06:52:18 CDT)
  - RE: [AMBER] Chirality error in pdb xiawei (Fri Aug 28 2009 - 01:41:45 CDT)
    - Re: [AMBER] Chirality error in pdb case (Fri Aug 28 2009 - 06:33:41 CDT)
[AMBER] ZPVE simple question ondrej.prenosil_at_marge.uochb.cas.cz (Wed Aug 26 2009 - 04:42:04 CDT)
- Re: [AMBER] ZPVE simple question Jerome.GOLEBIOWSKI_at_unice.fr (Wed Aug 26 2009 - 06:15:00 CDT)
- Re: [AMBER] ZPVE simple question case (Wed Aug 26 2009 - 06:41:27 CDT)
[AMBER] Need you help bharat lakhani (Wed Aug 26 2009 - 08:41:17 CDT)
- Re: [AMBER] Need you help Carlos Simmerling (Wed Aug 26 2009 - 08:48:20 CDT)
[AMBER] Re: question_on_MMPBSA jackie (Wed Aug 26 2009 - 10:08:01 CDT)
- RE: [AMBER] Re: question_on_MMPBSA Catein Catherine (Thu Aug 27 2009 - 00:55:59 CDT)
  - Re: [AMBER] Re: question_on_MMPBSA jackie (Thu Aug 27 2009 - 10:41:28 CDT)
[AMBER] Inquiries about antechamber Yikan Chen (Wed Aug 26 2009 - 12:07:20 CDT)
- Re: [AMBER] Inquiries about antechamber Nicholas Musolino (Wed Aug 26 2009 - 16:02:21 CDT)
  - Re: [AMBER] Inquiries about antechamber Yikan Chen (Wed Aug 26 2009 - 21:05:40 CDT)
    - Re: [AMBER] Inquiries about antechamber FyD (Thu Aug 27 2009 - 01:15:55 CDT)
  - Re: [AMBER] Inquiries about antechamber jackie (Thu Aug 27 2009 - 10:48:24 CDT)
[AMBER] SCC-DFTB MD for mercury ions in proteins Vaida Arciðauskaitë (Thu Aug 27 2009 - 11:41:17 CDT)
- Re: [AMBER] SCC-DFTB MD for mercury ions in proteins Adrian Roitberg (Thu Aug 27 2009 - 11:51:21 CDT)
[AMBER] Setting a constrain in one direction Darren Yang (Thu Aug 27 2009 - 22:15:30 CDT)
- Re: [AMBER] Setting a constrain in one direction Nicholas Musolino (Thu Aug 27 2009 - 22:40:54 CDT)
- RE: [AMBER] Setting a constrain in one direction matthew_seetin_at_urmc.rochester.edu (Fri Aug 28 2009 - 09:35:57 CDT)
  - [AMBER] nmr restraint for angle between vectors Peter Varnai (Fri Aug 28 2009 - 20:10:20 CDT)
[AMBER] Regarding principal component analysis using ptraj Arvind Marathe (Fri Aug 28 2009 - 01:54:40 CDT)
- Re: [AMBER] Regarding principal component analysis using ptraj Hannes Loeffler (Fri Aug 28 2009 - 02:28:29 CDT)
  - Re: [AMBER] Regarding principal component analysis using ptraj Arvind Marathe (Fri Aug 28 2009 - 06:04:22 CDT)
    - Re: [AMBER] Regarding principal component analysis using ptraj Hannes Loeffler (Fri Aug 28 2009 - 06:45:05 CDT)
    - Re: [AMBER] Regarding principal component analysis using ptraj Arvind Marathe (Fri Aug 28 2009 - 06:56:53 CDT)
[AMBER] (no subject) workalemahu berhanu (Fri Aug 28 2009 - 09:06:56 CDT)
- Re: [AMBER] (no subject) workalemahu berhanu (Fri Aug 28 2009 - 11:22:31 CDT)
[AMBER] about file format Jia Xu (Sat Aug 29 2009 - 02:55:49 CDT)
- Re: [AMBER] about file format Tom Joseph (Sat Aug 29 2009 - 09:50:37 CDT)
  - Re: [AMBER] about file format Jia Xu (Sun Aug 30 2009 - 00:32:30 CDT)
[AMBER] radius for Manganese ion Chunliyan (Sat Aug 29 2009 - 09:43:00 CDT)
- Re: [AMBER] radius for Manganese ion E.M. (Sun Aug 30 2009 - 18:38:38 CDT)
[AMBER] Dyndom Chunliyan (Sat Aug 29 2009 - 09:43:00 CDT)
- Re: [AMBER] Dyndom Carlos Simmerling (Sat Aug 29 2009 - 09:59:23 CDT)
- RE: [AMBER] Dyndom Loeffler, Hannes (STFC,DL,CSE) (Sat Aug 29 2009 - 10:18:18 CDT)
[AMBER] (no subject) workalemahu berhanu (Sat Aug 29 2009 - 10:29:34 CDT)
- Re: [AMBER] (no subject) workalemahu berhanu (Mon Aug 31 2009 - 00:19:27 CDT)
[AMBER] problem with 4-Hydroxyl-Proline tutorial Jia Xu (Sun Aug 30 2009 - 02:46:18 CDT)
- Re: [AMBER] problem with 4-Hydroxyl-Proline tutorial FyD (Mon Aug 31 2009 - 15:10:52 CDT)
  - Re: [AMBER] problem with 4-Hydroxyl-Proline tutorial Jia Xu (Tue Sep 01 2009 - 00:10:50 CDT)
[AMBER] Changing pH of the system nicholus bhattacharjee (Sun Aug 30 2009 - 06:13:17 CDT)
- Re: [AMBER] Changing pH of the system Adrian Roitberg (Sun Aug 30 2009 - 10:26:01 CDT)
  - Re: [AMBER] Changing pH of the system nicholus bhattacharjee (Sun Aug 30 2009 - 10:40:42 CDT)
[AMBER] How to derive charges from the output bharat lakhani (Mon Aug 31 2009 - 00:33:21 CDT)
- Re: [AMBER] How to derive charges from the output Barbault Florent (Mon Aug 31 2009 - 02:38:09 CDT)
  - Re: [AMBER] How to derive charges from the output bharat lakhani (Mon Aug 31 2009 - 08:43:15 CDT)
    - Re: [AMBER] How to derive charges from the output FyD (Mon Aug 31 2009 - 15:35:46 CDT)
    - Re: [AMBER] How to derive charges from the output bharat lakhani (Tue Sep 01 2009 - 03:46:12 CDT)
[AMBER] Query regarding watershell command Mannan (Mon Aug 31 2009 - 05:38:08 CDT)
- [AMBER] How to remove Hydrogen using ptraj Mannan (Tue Sep 01 2009 - 05:50:44 CDT)
  - Re: [AMBER] How to remove Hydrogen using ptraj Thomas Cheatham III (Tue Sep 01 2009 - 10:55:43 CDT)
    - Re: [AMBER] How to remove Hydrogen using ptraj case (Tue Sep 01 2009 - 12:19:51 CDT)
    - Re: [AMBER] How to remove Hydrogen using ptraj Thomas Cheatham III (Tue Sep 01 2009 - 12:25:10 CDT)
[AMBER] divcon question Andrei Neamtu (Mon Aug 31 2009 - 06:31:35 CDT)
- Re: [AMBER] divcon question case (Mon Aug 31 2009 - 07:34:14 CDT)
[AMBER] ATP/GTP parameters Steve Seibold (Mon Aug 31 2009 - 07:33:04 CDT)
- Re: [AMBER] ATP/GTP parameters case (Mon Aug 31 2009 - 07:41:22 CDT)
- Re: [AMBER] ATP/GTP parameters FyD (Mon Aug 31 2009 - 15:20:50 CDT)
[AMBER] GTP/ATP parameters Steve Seibold (Mon Aug 31 2009 - 07:44:56 CDT)
[AMBER] momentum in MD simulation dhacademic (Mon Aug 31 2009 - 09:37:42 CDT)
- Re: [AMBER] momentum in MD simulation case (Tue Sep 01 2009 - 06:48:52 CDT)
- Re: Re: [AMBER] momentum in MD simulation dhacademic (Wed Sep 02 2009 - 12:37:50 CDT)
[AMBER] antechamber bug report Matthew Walsh (Mon Aug 31 2009 - 11:43:08 CDT)
- Re: [AMBER] antechamber bug report case (Mon Aug 31 2009 - 12:36:33 CDT)
[AMBER] Docking with Amber Jordan, Brad (Mon Aug 31 2009 - 15:01:15 CDT)
- Re: [AMBER] Docking with Amber case (Mon Aug 31 2009 - 19:58:49 CDT)
[AMBER] ACE and NME patch: VMD ??? Siddharth Rastogi (Mon Aug 31 2009 - 19:25:47 CDT)
- RE: [AMBER] ACE and NME patch: VMD ??? Ross Walker (Tue Sep 01 2009 - 12:54:38 CDT)
[AMBER] how to pull a dna balaji nagarajan (Mon Aug 31 2009 - 21:39:10 CDT)
- Re: [AMBER] how to pull a dna Sam Danziger (Tue Sep 01 2009 - 06:17:09 CDT)
[AMBER] symbol lookup error Bala subramanian (Tue Sep 01 2009 - 03:43:51 CDT)
- RE: [AMBER] symbol lookup error Ross Walker (Tue Sep 01 2009 - 14:42:49 CDT)
[AMBER] how to pull a dna balaji nagarajan (Tue Sep 01 2009 - 09:24:29 CDT)
[AMBER] Reg. snapshot_statistics.out.snap Rose Tamil (Tue Sep 01 2009 - 12:04:08 CDT)
[AMBER] Creating new counterions Timothy Robbins (trobbins) (Tue Sep 01 2009 - 14:00:37 CDT)
- Re: [AMBER] Creating new counterions case (Tue Sep 01 2009 - 15:03:48 CDT)
  - [AMBER] Question regarding PCA analysis. Catein Catherine (Tue Sep 01 2009 - 22:53:10 CDT)
Re: [AMBER] Creating new counterions Bill Ross (Tue Sep 01 2009 - 14:58:55 CDT)
[AMBER] Simulation short peptide and protein interaction Rilei Yu (Tue Sep 01 2009 - 19:50:29 CDT)
- Re: [AMBER] Simulation short peptide and protein interaction case (Wed Sep 02 2009 - 07:15:06 CDT)
  - [AMBER] How to find water-mediated hydrogen bond? Catein Catherine (Wed Sep 02 2009 - 09:10:37 CDT)
    - Re: [AMBER] How to find water-mediated hydrogen bond? Hannes Loeffler (Thu Sep 03 2009 - 02:53:51 CDT)
  - Re: [AMBER] Simulation short peptide and protein interaction Rilei Yu (Thu Sep 03 2009 - 07:22:10 CDT)
    - Re: [AMBER] Simulation short peptide and protein interaction Carlos Simmerling (Thu Sep 03 2009 - 08:34:27 CDT)
[AMBER] question about ptraj Jeffrey (Wed Sep 02 2009 - 03:20:12 CDT)
- RE: [AMBER] question about ptraj Niel Henriksen (Wed Sep 02 2009 - 09:37:39 CDT)
[AMBER] how to give force values in TMD balaji nagarajan (Wed Sep 02 2009 - 05:03:41 CDT)
[AMBER] Active site - Ion - Search engine s. Bill (Wed Sep 02 2009 - 09:53:39 CDT)
[AMBER] What is dual topology Ashish Runthala (Wed Sep 02 2009 - 10:25:19 CDT)
- Re: [AMBER] What is dual topology case (Wed Sep 02 2009 - 10:48:51 CDT)
[AMBER] How to consider the off centre charges Ashish Runthala (Wed Sep 02 2009 - 10:28:40 CDT)
- Re: [AMBER] How to consider the off centre charges case (Wed Sep 02 2009 - 10:50:12 CDT)
[AMBER] unit of force constant balaji nagarajan (Wed Sep 02 2009 - 11:57:25 CDT)
[AMBER] antechamber bug: output of incorrect bond character Matthew Walsh (Wed Sep 02 2009 - 13:37:44 CDT)
- Re: [AMBER] antechamber bug: output of incorrect bond character case (Wed Sep 02 2009 - 20:53:37 CDT)
  - Re: [AMBER] antechamber bug: output of incorrect bond character Matthew Walsh (Wed Sep 02 2009 - 23:30:04 CDT)
[AMBER] Question about the debug forces Faezeh Salehi (Wed Sep 02 2009 - 16:30:47 CDT)
[AMBER] how to deal with aromatic nitro group with antechamber Lin Xu (Wed Sep 02 2009 - 17:04:13 CDT)
- Re: [AMBER] how to deal with aromatic nitro group with antechamber case (Wed Sep 02 2009 - 21:15:14 CDT)
[AMBER] Heme + Fe(II) + O2 + histidine parameter Haining Liu (Wed Sep 02 2009 - 22:36:31 CDT)
- Re: [AMBER] Heme + Fe(II) + O2 + histidine parameter FyD (Thu Sep 03 2009 - 02:03:45 CDT)
  - Re: [AMBER] Heme + Fe(II) + O2 + histidine parameter Haining Liu (Thu Sep 03 2009 - 16:13:09 CDT)
    - Re: [AMBER] Heme + Fe(II) + O2 + histidine parameter FyD (Fri Sep 04 2009 - 02:43:00 CDT)
[AMBER] ATP and GTP parameters E.M. (Thu Sep 03 2009 - 00:29:47 CDT)
- Re: [AMBER] ATP and GTP parameters FyD (Thu Sep 03 2009 - 01:15:54 CDT)
  - Re: [AMBER] ATP and GTP parameters E.M. (Thu Sep 03 2009 - 01:30:31 CDT)
[AMBER] What should be the standard input file when imin=5 Ashish Runthala (Thu Sep 03 2009 - 02:25:49 CDT)
- Re: [AMBER] What should be the standard input file when imin=5 Carlos Simmerling (Thu Sep 03 2009 - 06:55:48 CDT)
[AMBER] QM/MM simulation gaurav panwar (Thu Sep 03 2009 - 15:11:42 CDT)
- RE: [AMBER] QM/MM simulation Ross Walker (Thu Sep 03 2009 - 15:43:45 CDT)
[AMBER] Problem about adding a small residue to DNA Yikan Chen (Thu Sep 03 2009 - 23:33:52 CDT)
- å›žå¤ï¼š [AMBER] Problem about adding a small residue to DNA Rilei Yu (Fri Sep 04 2009 - 01:33:50 CDT)
  - Re: »Ø¸´£º [AMBER] Problem about adding a small residue to DNA Yikan Chen (Fri Sep 04 2009 - 14:51:38 CDT)
- Re: [AMBER] Problem about adding a small residue to DNA case (Fri Sep 04 2009 - 14:32:53 CDT)
[AMBER] Kinetics Soumya Lipsa Rath (Fri Sep 04 2009 - 01:39:54 CDT)
- Re: [AMBER] Kinetics case (Fri Sep 04 2009 - 14:29:24 CDT)
  - Re: [AMBER] Kinetics Soumya Lipsa Rath (Tue Sep 08 2009 - 01:36:18 CDT)
    - [AMBER] Enquiry about MM/GBSA output file. Catein Catherine (Tue Sep 08 2009 - 02:14:19 CDT)
[AMBER] prep file Jio M (Fri Sep 04 2009 - 04:24:04 CDT)
- Re: [AMBER] prep file case (Fri Sep 04 2009 - 09:09:06 CDT)
[AMBER] Dummy atoms and MM-PBSA Alireza Shaneh (Fri Sep 04 2009 - 11:48:16 CDT)
- Re: [AMBER] Dummy atoms and MM-PBSA Ray Luo (Fri Sep 04 2009 - 13:25:33 CDT)
[AMBER] nmropt option Jio M (Fri Sep 04 2009 - 13:05:25 CDT)
- Re: [AMBER] nmropt option Carlos Simmerling (Fri Sep 04 2009 - 13:15:13 CDT)
  - Re: [AMBER] nmropt option Jio M (Sat Sep 05 2009 - 00:23:09 CDT)
    - Re: [AMBER] nmropt option Carlos Simmerling (Sat Sep 05 2009 - 05:59:04 CDT)
[AMBER] Provisional Support for AMBER 10 PMEMD on NVIDIA GPUs Ross Walker (Fri Sep 04 2009 - 13:51:44 CDT)
[AMBER] Antechamber generate a prep file in a wrong order... Yikan Chen (Sat Sep 05 2009 - 14:37:53 CDT)
- Re: [AMBER] Antechamber generate a prep file in a wrong order... case (Sun Sep 06 2009 - 07:26:02 CDT)
[AMBER] How to find a protein's energy Ashish Runthala (Sat Sep 05 2009 - 22:48:01 CDT)
- Re: [AMBER] How to find a protein's energy Carlos Simmerling (Sun Sep 06 2009 - 06:49:53 CDT)
  - Re: [AMBER] How to find a protein's energy Ashish Runthala (Sun Sep 06 2009 - 07:30:26 CDT)
[AMBER] R.E.D. : Gaussian Error manoj singh (Sun Sep 06 2009 - 13:40:48 CDT)
- Re: [AMBER] R.E.D. : Gaussian Error FyD (Sun Sep 06 2009 - 14:41:41 CDT)
  - Re: [AMBER] R.E.D. : Gaussian Error manoj singh (Sun Sep 06 2009 - 23:22:44 CDT)
    - Re: [AMBER] R.E.D. : Gaussian Error FyD (Mon Sep 07 2009 - 00:07:34 CDT)
    - Re: [AMBER] R.E.D. : Gaussian Error manoj singh (Mon Sep 07 2009 - 00:46:54 CDT)
[AMBER] (no subject) gunajyoti das (Mon Sep 07 2009 - 04:21:45 CDT)
[AMBER] problem in QM/MM input file gaurav panwar (Mon Sep 07 2009 - 12:33:20 CDT)
- Re: [AMBER] problem in QM/MM input file Tom Joseph (Tue Sep 08 2009 - 07:37:56 CDT)
[AMBER] loadpdb Jagdeesh C (Mon Sep 07 2009 - 12:36:58 CDT)
- Re: [AMBER] loadpdb Carlos Simmerling (Mon Sep 07 2009 - 13:01:10 CDT)
  - Re: [AMBER] loadpdb Jagdeesh C (Mon Sep 07 2009 - 13:31:42 CDT)
- Re: [AMBER] loadpdb Bill Ross (Tue Sep 08 2009 - 11:58:12 CDT)
  - Re: [AMBER] loadpdb Jagdeesh C (Tue Sep 08 2009 - 20:55:36 CDT)
- Re: [AMBER] loadpdb Bill Ross (Tue Sep 08 2009 - 21:53:32 CDT)
[AMBER] general query: implicit solvation Jio M (Tue Sep 08 2009 - 04:28:49 CDT)
- Re: [AMBER] general query: implicit solvation Carlos Simmerling (Tue Sep 08 2009 - 05:11:24 CDT)
[AMBER] loading PDB of a RNA sequence gunajyoti das (Tue Sep 08 2009 - 05:31:47 CDT)
- Re: [AMBER] loading PDB of a RNA sequence Carlos Simmerling (Tue Sep 08 2009 - 05:33:57 CDT)
- Re: [AMBER] loading PDB of a RNA sequence case (Tue Sep 08 2009 - 06:38:34 CDT)
[AMBER] No sp2 improper torsion term for NB-CA-CB-CB qiaoyan (Tue Sep 08 2009 - 07:29:17 CDT)
- Re: [AMBER] No sp2 improper torsion term for NB-CA-CB-CB case (Tue Sep 08 2009 - 07:58:33 CDT)
[AMBER] unit of force constant balaji nagarajan (Tue Sep 08 2009 - 08:16:08 CDT)
- Re: [AMBER] unit of force constant Carlos Simmerling (Tue Sep 08 2009 - 08:21:40 CDT)
  - RE: [AMBER] unit of force constant balaji nagarajan (Tue Sep 08 2009 - 08:41:37 CDT)
[AMBER] How to denature DNA balaji nagarajan (Tue Sep 08 2009 - 09:00:43 CDT)
- Re: [AMBER] How to denature DNA Adrian Roitberg (Tue Sep 08 2009 - 09:04:30 CDT)
  - RE: [AMBER] How to denature DNA balaji nagarajan (Tue Sep 08 2009 - 11:29:57 CDT)
- RE: [AMBER] How to denature DNA Bill Ross (Tue Sep 08 2009 - 12:33:09 CDT)
  - RE: [AMBER] How to denature DNA balaji nagarajan (Tue Sep 08 2009 - 23:01:55 CDT)
- RE: [AMBER] How to denature DNA Bill Ross (Wed Sep 09 2009 - 11:38:04 CDT)
  - RE: [AMBER] How to denature DNA balaji nagarajan (Wed Sep 09 2009 - 12:14:37 CDT)
[AMBER] AmberTools 1.3 / CHAMBER Mag. Thomas Taylor (Tue Sep 08 2009 - 09:29:23 CDT)
[AMBER] amoeba.prm problem? Ivan Gladich (Tue Sep 08 2009 - 09:31:43 CDT)
- Re: [AMBER] amoeba.prm problem? case (Wed Sep 09 2009 - 14:17:39 CDT)
  - Re: [AMBER] amoeba.prm problem? Ivan Gladich (Fri Sep 11 2009 - 15:34:07 CDT)
    - Re: [AMBER] amoeba.prm problem? case (Sat Sep 12 2009 - 08:46:52 CDT)
    - Re: [AMBER] amoeba.prm problem? Ivan Gladich (Fri Sep 18 2009 - 14:57:39 CDT)
[AMBER] TI in Amber9/10 Alessandro S. Nascimento (Tue Sep 08 2009 - 10:47:26 CDT)
- Re: [AMBER] TI in Amber9/10 steinbrt_at_rci.rutgers.edu (Tue Sep 08 2009 - 12:41:32 CDT)
- Re: [AMBER] TI in Amber9/10 Ilyas Yildirim (Tue Sep 08 2009 - 13:07:40 CDT)
Re: [AMBER] loadpdb Bill Ross (Tue Sep 08 2009 - 11:53:03 CDT)
[AMBER] logdvdl does not work helde010_at_umn.edu (Tue Sep 08 2009 - 11:53:14 CDT)
- Re: [AMBER] logdvdl does not work steinbrt_at_rci.rutgers.edu (Tue Sep 08 2009 - 12:37:31 CDT)
[AMBER] loading a following attached protein in amber 10 albert albert (Tue Sep 08 2009 - 12:09:09 CDT)
- Re: [AMBER] loading a following attached protein in amber 10 David Watson (Tue Sep 08 2009 - 12:26:19 CDT)
- Re: [AMBER] loading a following attached protein in amber 10 case (Tue Sep 08 2009 - 12:27:47 CDT)
  - Re: [AMBER] loading a following attached protein in amber 10 albert albert (Tue Sep 08 2009 - 12:43:55 CDT)
[AMBER] QMMM NEB with PM3-PDDG fails with ASSERTion 'ierr.eq.0' pimd_init.f line 320 Keith Van Nostrand (Tue Sep 08 2009 - 14:26:14 CDT)
- Re: [AMBER] QMMM NEB with PM3-PDDG fails with ASSERTion 'ierr.eq.0' pimd_init.f line 320 case (Sat Sep 12 2009 - 09:17:16 CDT)
[AMBER] Hbond analysis: Direction of the hydrogen Age.Skjevik_at_biomed.uib.no (Tue Sep 08 2009 - 14:45:19 CDT)
- Re: [AMBER] Hbond analysis: Direction of the hydrogen Shulin Zhuang (Tue Sep 08 2009 - 14:54:22 CDT)
  - Re: [AMBER] Hbond analysis: Direction of the hydrogen Age.Skjevik_at_biomed.uib.no (Tue Sep 08 2009 - 16:56:50 CDT)
[AMBER] Leap warning manoj singh (Wed Sep 09 2009 - 00:38:33 CDT)
- Re: [AMBER] Leap warning Ashish Runthala (Wed Sep 09 2009 - 02:21:03 CDT)
- Re: [AMBER] Leap warning case (Wed Sep 09 2009 - 06:31:36 CDT)
- Re: [AMBER] Leap warning Bill Ross (Wed Sep 09 2009 - 11:49:05 CDT)
[AMBER] about the number of residues after MD Qinghua Liao (Wed Sep 09 2009 - 02:23:03 CDT)
[AMBER] PK zero for specific dihedral and parmchk Loeffler, Hannes (STFC,DL,CSE) (Wed Sep 09 2009 - 03:00:20 CDT)
- Re: [AMBER] PK zero for specific dihedral and parmchk Carlos Simmerling (Wed Sep 09 2009 - 05:23:31 CDT)
- Re: [AMBER] PK zero for specific dihedral and parmchk case (Wed Sep 09 2009 - 06:32:51 CDT)
[AMBER] gaff.dat questions gilbert_at_bluemarble.net (Wed Sep 09 2009 - 09:02:28 CDT)
- Re: [AMBER] gaff.dat questions case (Wed Sep 09 2009 - 09:16:23 CDT)
[AMBER] parameterization of protein-ligand complex cc cc (Wed Sep 09 2009 - 11:29:07 CDT)
- Re: [AMBER] parameterization of protein-ligand complex case (Wed Sep 09 2009 - 11:39:05 CDT)
  - RE: [AMBER] parameterization of protein-ligand complex cc cc (Wed Sep 09 2009 - 12:44:17 CDT)
- RE: [AMBER] parameterization of protein-ligand complex Jeff Yeo (Mon Sep 14 2009 - 10:03:25 CDT)
Re: [AMBER] parameterization of protein-ligand complex Bill Ross (Wed Sep 09 2009 - 12:12:28 CDT)
- RE: [AMBER] parameterization of protein-ligand complex cc cc (Wed Sep 09 2009 - 12:41:52 CDT)
[AMBER] Problem with GROUP input Jordan, Brad (Wed Sep 09 2009 - 18:58:36 CDT)
- [AMBER] RE: Problem with GROUP input Jordan, Brad (Wed Sep 09 2009 - 19:11:51 CDT)
[AMBER] Solvate in an alkaline solution vallespardojl_at_chem.leidenuniv.nl (Thu Sep 10 2009 - 03:07:07 CDT)
- Re: [AMBER] Solvate in an alkaline solution case (Thu Sep 10 2009 - 07:05:44 CDT)
[AMBER] input file Mag. Thomas Taylor (Thu Sep 10 2009 - 05:48:06 CDT)
- Re: [AMBER] input file Carlos Simmerling (Thu Sep 10 2009 - 06:03:17 CDT)
  - Re: [AMBER] input file / skinnb Mag. Thomas Taylor (Wed Sep 16 2009 - 02:49:32 CDT)
  - [AMBER] hbond analysis qiaoyan (Thu Dec 31 2009 - 02:40:22 CST)
- Re: [AMBER] input file Jenny Iskrenova (Thu Sep 10 2009 - 08:05:03 CDT)
  - Re: [AMBER] input file Ashish Runthala (Thu Sep 10 2009 - 09:05:32 CDT)
[AMBER] QM/MM minimization gaurav panwar (Thu Sep 10 2009 - 09:05:37 CDT)
Re: [AMBER] input file Bill Ross (Thu Sep 10 2009 - 11:51:10 CDT)
[AMBER] question with radial distribution function Ganesh Kamath (Thu Sep 10 2009 - 17:08:34 CDT)
[AMBER] periodic boundary condition for implicit solvent simulation and SHORT command Workalemahu Berhanu (Thu Sep 10 2009 - 17:37:32 CDT)
- Re: [AMBER] periodic boundary condition for implicit solvent simulation and SHORT command case (Thu Sep 10 2009 - 21:04:53 CDT)
[AMBER] DMF solvent box Abhishek Banerjee (Thu Sep 10 2009 - 21:40:21 CDT)
- Re: [AMBER] DMF solvent box Jio M (Fri Sep 11 2009 - 10:00:40 CDT)
- Re: [AMBER] DMF solvent box FyD (Sat Sep 12 2009 - 09:07:30 CDT)
  - Re: [AMBER] DMF solvent box Abhishek Banerjee (Sun Sep 13 2009 - 00:33:39 CDT)
  - Re: [AMBER] DMF solvent box Abhishek Banerjee (Sun Sep 13 2009 - 03:56:18 CDT)
    - Re: [AMBER] DMF solvent box FyD (Sun Sep 13 2009 - 04:25:33 CDT)
- Re: [AMBER] DMF solvent box Abhishek Banerjee (Sun Sep 13 2009 - 09:24:04 CDT)
  - Re: [AMBER] DMF solvent box FyD (Sun Sep 13 2009 - 12:01:13 CDT)
- Re: [AMBER] DMF solvent box Abhishek Banerjee (Mon Sep 14 2009 - 08:18:30 CDT)
  - Re: [AMBER] DMF solvent box FyD (Mon Sep 14 2009 - 10:04:58 CDT)
    - Re: [AMBER] DMF solvent box Abhishek Banerjee (Tue Sep 15 2009 - 23:33:23 CDT)
    - Re: [AMBER] DMF solvent box FyD (Wed Sep 16 2009 - 00:09:42 CDT)
- Re: [AMBER] DMF solvent box Abhishek Banerjee (Thu Sep 17 2009 - 01:15:53 CDT)
  - Re: [AMBER] DMF solvent box FyD (Thu Sep 17 2009 - 02:00:06 CDT)
    - Re: [AMBER] DMF solvent box Abhishek Banerjee (Sat Sep 19 2009 - 00:24:08 CDT)
    - Re: [AMBER] DMF solvent box FyD (Sat Sep 19 2009 - 01:36:20 CDT)
- Re: [AMBER] DMF solvent box Abhishek Banerjee (Tue Oct 06 2009 - 23:10:22 CDT)
  - Re: [AMBER] DMF solvent box FyD (Wed Oct 07 2009 - 15:34:35 CDT)
- Re: [AMBER] DMF solvent box Abhishek Banerjee (Thu Oct 08 2009 - 22:41:02 CDT)
  - Re: [AMBER] DMF solvent box FyD (Thu Oct 08 2009 - 23:08:59 CDT)
[AMBER] PBSA for gp41 binding free energy shuqing wang (Fri Sep 11 2009 - 01:42:59 CDT)
- Re: [AMBER] PBSA for gp41 binding free energy Ray Luo (Fri Sep 11 2009 - 20:59:07 CDT)
[AMBER] dihedral force calculation Germain Vallverdu (Fri Sep 11 2009 - 09:35:08 CDT)
- Re: [AMBER] dihedral force calculation case (Sat Sep 12 2009 - 09:04:34 CDT)
[AMBER] RESP RED s. Bill (Fri Sep 11 2009 - 13:40:24 CDT)
- Re: [AMBER] RESP RED FyD (Sat Sep 12 2009 - 09:35:16 CDT)
[AMBER] charge consideration Jio M (Fri Sep 11 2009 - 15:17:34 CDT)
- Re: [AMBER] charge consideration case (Sat Sep 12 2009 - 08:59:56 CDT)
[AMBER] "nan" in gaussian input files generated by antechamber Yikan Chen (Fri Sep 11 2009 - 15:19:04 CDT)
- Re: [AMBER] "nan" in gaussian input files generated by antechamber case (Sat Sep 12 2009 - 08:55:14 CDT)
- Re: [AMBER] "nan" in gaussian input files generated by antechamber FyD (Sat Sep 12 2009 - 09:58:52 CDT)
[AMBER] What is the Optimum Ph for solvating a protein Ashish Runthala (Sun Sep 13 2009 - 08:08:40 CDT)
- Re: [AMBER] What is the Optimum Ph for solvating a protein case (Sun Sep 13 2009 - 16:19:24 CDT)
[AMBER] load .crd & .top in xleap vallespardojl_at_chem.leidenuniv.nl (Sun Sep 13 2009 - 09:21:15 CDT)
- Re: [AMBER] load .crd & .top in xleap oguz gurbulak (Sun Sep 13 2009 - 14:20:26 CDT)
[AMBER] re: charge interaction Jio M (Sun Sep 13 2009 - 09:38:43 CDT)
- Re: [AMBER] re: charge interaction case (Sun Sep 13 2009 - 16:13:19 CDT)
  - Re: [AMBER] re: charge interaction case (Sun Sep 13 2009 - 16:37:55 CDT)
[AMBER] variable header for ABMD stephane acoca (Sun Sep 13 2009 - 22:03:00 CDT)
[AMBER] re: charge consideration Jio M (Mon Sep 14 2009 - 03:38:27 CDT)
[AMBER] How to prepare the coordinate and toplogy files in leap ? xuemeiwang1103 (Mon Sep 14 2009 - 04:03:59 CDT)
- Re: [AMBER] How to prepare the coordinate and toplogy files in leap ? case (Mon Sep 14 2009 - 06:56:08 CDT)
[AMBER] error xleap: XaLeap_wcl is empty Mari Carmen Pérez (Mon Sep 14 2009 - 04:59:09 CDT)
- Re: [AMBER] error xleap: XaLeap_wcl is empty case (Mon Sep 14 2009 - 07:02:12 CDT)
[AMBER] Ki and G s. Bill (Mon Sep 14 2009 - 06:39:20 CDT)
- Re: [AMBER] Ki and G steinbrt_at_rci.rutgers.edu (Mon Sep 14 2009 - 06:59:40 CDT)
  - Re: [AMBER] Ki and G Adrian Roitberg (Mon Sep 14 2009 - 09:28:57 CDT)
  - Re: [AMBER] Ki and G Marek Maly (Mon Sep 14 2009 - 12:02:36 CDT)
[AMBER] Carbon Nanotube Library file (CNT) Christopher Stiles (Mon Sep 14 2009 - 08:59:57 CDT)
[AMBER] radial distribution function in amber Ganesh Kamath (Mon Sep 14 2009 - 09:58:56 CDT)
[AMBER] Question on ECAVITY term of MM_PBSA Gianluca Degliesposti (Mon Sep 14 2009 - 10:28:12 CDT)
[AMBER] makeDIST_RST: no map function Workalemahu Berhanu (Mon Sep 14 2009 - 14:30:15 CDT)
- RE: [AMBER] makeDIST_RST: no map function Duggan, Brendan M. (Tue Sep 15 2009 - 08:40:00 CDT)
- Re: [AMBER] makeDIST_RST: no map function case (Tue Sep 15 2009 - 09:38:23 CDT)
  - Re: [AMBER] makeDIST_RST: no map function Workalemahu Berhanu (Tue Sep 15 2009 - 10:11:27 CDT)
  - Re: [AMBER] makeDIST_RST: no map function Workalemahu Berhanu (Tue Sep 15 2009 - 10:24:56 CDT)
[AMBER] Problem on PMEMD zyxism (Mon Sep 14 2009 - 20:11:57 CDT)
- Re: [AMBER] Problem on PMEMD Tom Joseph (Mon Sep 14 2009 - 20:34:11 CDT)
[AMBER] Error in minimal xuemeiwang1103 (Tue Sep 15 2009 - 02:27:18 CDT)
- Re: [AMBER] Error in minimal case (Tue Sep 15 2009 - 06:56:02 CDT)
  - Re:Re: [AMBER] Error in minimal xuemeiwang1103 (Tue Sep 15 2009 - 08:54:58 CDT)
    - Re: Re: [AMBER] Error in minimal case (Tue Sep 15 2009 - 17:15:06 CDT)
[AMBER] problem running pmemd gbrna tests wong105_at_llnl.gov (Tue Sep 15 2009 - 13:07:14 CDT)
[AMBER] can antechamber convert a prep file from cartesian to internal coordinates? Paul Ledbetter (Tue Sep 15 2009 - 15:25:56 CDT)
- Re: [AMBER] can antechamber convert a prep file from cartesian to internal coordinates? case (Tue Sep 15 2009 - 17:12:25 CDT)
  - Re: [AMBER] can antechamber convert a prep file from cartesian to internal coordinates? Paul Ledbetter (Tue Sep 15 2009 - 18:34:54 CDT)
- Re: [AMBER] can antechamber convert a prep file from cartesian to internal coordinates? Bill Ross (Tue Sep 15 2009 - 17:15:38 CDT)
  - Re: [AMBER] can antechamber convert a prep file from cartesian to internal coordinates? Paul Ledbetter (Tue Sep 15 2009 - 18:40:09 CDT)
[AMBER] About the PMEMD compiling for CUDA wang (Wed Sep 16 2009 - 00:17:52 CDT)
- RE: [AMBER] About the PMEMD compiling for CUDA Ross Walker (Wed Sep 16 2009 - 01:55:11 CDT)
[AMBER] About the PMEMD compiling for CUDA Ross Walker (Wed Sep 16 2009 - 00:26:19 CDT)
[AMBER] database Steve Seibold (Wed Sep 16 2009 - 09:59:14 CDT)
- Re: [AMBER] database case (Wed Sep 16 2009 - 10:26:24 CDT)
  - RE: [AMBER] database Steve Seibold (Wed Sep 16 2009 - 11:11:47 CDT)
- RE: [AMBER] database Bill Ross (Wed Sep 16 2009 - 12:54:47 CDT)
  - [AMBER] antechamber error Taufik Al-Sarraj (Wed Sep 16 2009 - 13:18:32 CDT)
  - RE: [AMBER] database FyD (Wed Sep 16 2009 - 13:58:38 CDT)
[AMBER] RDC analysis: "No restraint defined" Michael Durney (Wed Sep 16 2009 - 11:10:34 CDT)
- Re: [AMBER] RDC analysis: "No restraint defined" case (Wed Sep 16 2009 - 11:47:41 CDT)
[AMBER] question with hbond Ganesh Kamath (Wed Sep 16 2009 - 16:36:18 CDT)
[AMBER] loading RNA sequence in xleap gunajyoti das (Thu Sep 17 2009 - 03:27:49 CDT)
- Re: [AMBER] loading RNA sequence in xleap FyD (Thu Sep 17 2009 - 04:39:09 CDT)
- Re: [AMBER] loading RNA sequence in xleap case (Thu Sep 17 2009 - 07:13:38 CDT)
[AMBER] PES QM and MM s. Bill (Thu Sep 17 2009 - 05:53:46 CDT)
[AMBER] Force Field Fitting s. Bill (Thu Sep 17 2009 - 06:36:33 CDT)
- Re: [AMBER] Force Field Fitting manoj singh (Thu Sep 17 2009 - 12:20:50 CDT)
  - [AMBER] Discrepancy between AMBER and VMD calculation Sunita Patel (Thu Sep 17 2009 - 14:11:07 CDT)
  - Re: [AMBER] Force Field Fitting s. Bill (Thu Sep 17 2009 - 14:27:46 CDT)
    - Re: [AMBER] Force Field Fitting manoj singh (Thu Sep 17 2009 - 14:32:33 CDT)
[AMBER] install ambertools Karl Kirschner (Thu Sep 17 2009 - 07:55:22 CDT)
- Re: [AMBER] install ambertools case (Thu Sep 17 2009 - 08:40:28 CDT)
[AMBER] NAB syntax Michael Durney (Thu Sep 17 2009 - 09:58:58 CDT)
- Re: [AMBER] NAB syntax Andreas Svrcek-Seiler (Thu Sep 17 2009 - 10:21:51 CDT)
- Re: [AMBER] NAB syntax case (Thu Sep 17 2009 - 10:22:29 CDT)
[AMBER] pH calculations Michael Durney (Thu Sep 17 2009 - 10:01:08 CDT)
Re: [AMBER] PES QM and MM Bill Ross (Thu Sep 17 2009 - 11:08:35 CDT)
[AMBER] how to ouput the electrostatic potential at a single atomic position? Jose Borreguero (Thu Sep 17 2009 - 14:06:54 CDT)
[AMBER] LINMIN failure notice Jio M (Fri Sep 18 2009 - 05:20:18 CDT)
- Re: [AMBER] LINMIN failure notice Ashish Runthala (Fri Sep 18 2009 - 05:46:09 CDT)
  - RE: [AMBER] LINMIN failure notice Ross Walker (Fri Sep 18 2009 - 18:41:33 CDT)
- Re: [AMBER] LINMIN failure notice case (Fri Sep 18 2009 - 06:38:33 CDT)
- Re: [AMBER] LINMIN failure notice Bill Ross (Fri Sep 18 2009 - 11:18:41 CDT)
[AMBER] PROBLEM WITH CHCL3BOX pdb Silvia Carlotto (Fri Sep 18 2009 - 07:49:12 CDT)
- Re: [AMBER] PROBLEM WITH CHCL3BOX pdb case (Fri Sep 18 2009 - 08:26:40 CDT)
  - Re: [AMBER] PROBLEM WITH CHCL3BOX pdb Hannes Loeffler (Fri Sep 18 2009 - 10:16:06 CDT)
    - Re: [AMBER] PROBLEM WITH CHCL3BOX pdb case (Fri Sep 18 2009 - 17:01:23 CDT)
[AMBER] how to make 50% aqueous TFE box? parul sharma (Fri Sep 18 2009 - 08:47:01 CDT)
- Re: [AMBER] how to make 50% aqueous TFE box? FyD (Fri Sep 18 2009 - 19:22:35 CDT)
[AMBER] Cygwin Home Directory Wallace Kunin (Fri Sep 18 2009 - 12:51:17 CDT)
- Re: [AMBER] Cygwin Home Directory Bill Ross (Fri Sep 18 2009 - 15:56:17 CDT)
  - Re: [AMBER] Cygwin Home Directory Wallace Kunin (Sat Sep 19 2009 - 11:13:20 CDT)
- Re: [AMBER] Cygwin Home Directory Bill Ross (Sat Sep 19 2009 - 12:29:59 CDT)
- Re: [AMBER] Cygwin Home Directory Bill Ross (Mon Sep 21 2009 - 12:45:02 CDT)
Re: [AMBER] Cygwin Home Directory Bill Ross (Fri Sep 18 2009 - 13:19:44 CDT)
- Re: [AMBER] Cygwin Home Directory Wallace Kunin (Fri Sep 18 2009 - 14:12:22 CDT)
  - Re: [AMBER] Cygwin Home Directory manoj singh (Fri Sep 18 2009 - 14:30:28 CDT)
[AMBER] warning in dispatchToken Jeff Yeo (Sun Sep 20 2009 - 05:30:57 CDT)
- Re: [AMBER] warning in dispatchToken case (Sun Sep 20 2009 - 08:14:49 CDT)
[AMBER] combining MD runs for post-MD analysis Jeff Yeo (Sun Sep 20 2009 - 19:02:12 CDT)
- Re: [AMBER] combining MD runs for post-MD analysis Qinghua Liao (Sun Sep 20 2009 - 20:01:22 CDT)
- Re: [AMBER] combining MD runs for post-MD analysis case (Sun Sep 20 2009 - 20:35:08 CDT)
[AMBER] Regarding united atom force field aneesh cna (Mon Sep 21 2009 - 05:17:20 CDT)
- Re: [AMBER] Regarding united atom force field Ray Luo (Mon Sep 21 2009 - 12:32:34 CDT)
- Re: [AMBER] Regarding united atom force field FyD (Tue Sep 22 2009 - 01:13:03 CDT)
[AMBER] problem building sander.apbs Oliver Kuhn (Mon Sep 21 2009 - 05:49:48 CDT)
- Re: [AMBER] problem building sander.apbs case (Mon Sep 21 2009 - 06:39:41 CDT)
- Re: [AMBER] problem building sander.apbs Oliver Kuhn (Mon Sep 21 2009 - 09:03:34 CDT)
  - Re: [AMBER] problem building sander.apbs case (Mon Sep 21 2009 - 09:38:20 CDT)
- Re: [AMBER] problem building sander.apbs Oliver Kuhn (Tue Sep 22 2009 - 03:10:10 CDT)
  - Re: [AMBER] problem building sander.apbs case (Tue Sep 22 2009 - 14:12:50 CDT)
  - Re: [AMBER] problem building sander.apbs Robert Konecny (Tue Sep 22 2009 - 14:55:40 CDT)
[AMBER] Question on ECAVITY term of MM_PBSA Gianluca Degliesposti (Mon Sep 21 2009 - 06:18:27 CDT)
- Re: [AMBER] Question on ECAVITY term of MM_PBSA Ray Luo (Mon Sep 21 2009 - 12:30:57 CDT)
- Re: [AMBER] Question on ECAVITY term of MM_PBSA Ray Luo (Mon Sep 21 2009 - 20:28:32 CDT)
[AMBER] generate prmtop file from CHARMM psf file Jeffrey (Mon Sep 21 2009 - 09:34:59 CDT)
Re: [AMBER] combining MD runs for post-MD analysis Bill Ross (Mon Sep 21 2009 - 12:32:53 CDT)
[AMBER] ACS COMP division awards- Oct 19th deadline Carlos Simmerling (Mon Sep 21 2009 - 12:49:28 CDT)
[AMBER] Installing AmberTools and Amber10 in Ubuntu - Instructions. David Dubins (Mon Sep 21 2009 - 18:02:47 CDT)
[AMBER] Pentane UA model aneesh cna (Tue Sep 22 2009 - 01:23:35 CDT)
- Re: [AMBER] Pentane UA model FyD (Tue Sep 22 2009 - 02:02:50 CDT)
Re: [AMBER] Installing AmberTools and Amber10 in Ubuntu - Instructions. oguz gurbulak (Tue Sep 22 2009 - 01:46:27 CDT)
[AMBER] RMSDf of heavy atoms Syed Tarique Moin (Tue Sep 22 2009 - 06:45:26 CDT)
[AMBER] Compiling Amber10 Williams, John (Tue Sep 22 2009 - 07:56:43 CDT)
[AMBER] ambertools and Snow Leopard 64 bits kernel Alan (Tue Sep 22 2009 - 08:55:25 CDT)
- Re: [AMBER] ambertools and Snow Leopard 64 bits kernel Tom Joseph (Tue Sep 22 2009 - 13:12:55 CDT)
  - Re: [AMBER] ambertools and Snow Leopard 64 bits kernel Alan (Tue Sep 22 2009 - 16:41:18 CDT)
  - Re: [AMBER] ambertools and Snow Leopard 64 bits kernel case (Wed Sep 23 2009 - 15:26:16 CDT)
[AMBER] Installation issue Ashveen Seenauth (Tue Sep 22 2009 - 11:17:49 CDT)
- Re: [AMBER] Installation issue Bill Ross (Tue Sep 22 2009 - 12:50:28 CDT)
- Re: [AMBER] Installation issue Bill Ross (Tue Sep 22 2009 - 12:55:34 CDT)
  - Re: [AMBER] Installation issue Ashveen Seenauth (Tue Sep 22 2009 - 12:59:46 CDT)
    - Re: [AMBER] Installation issue Tom Joseph (Tue Sep 22 2009 - 13:16:01 CDT)
- Re: [AMBER] Installation issue Bill Ross (Tue Sep 22 2009 - 12:59:22 CDT)
- Re: [AMBER] Installation issue Bill Ross (Tue Sep 22 2009 - 13:28:43 CDT)
  - Re: [AMBER] Installation issue Ashveen Seenauth (Wed Sep 23 2009 - 10:28:55 CDT)
- Re: [AMBER] Installation issue Bill Ross (Wed Sep 23 2009 - 11:29:28 CDT)
- Re: [AMBER] Installation issue Bill Ross (Wed Sep 23 2009 - 11:36:59 CDT)
Re: [AMBER] Installation issue Bill Ross (Tue Sep 22 2009 - 11:31:47 CDT)
- Re: [AMBER] Installation issue Ashveen Seenauth (Tue Sep 22 2009 - 11:45:13 CDT)
  - Re: [AMBER] Installation issue Tom Joseph (Tue Sep 22 2009 - 11:55:20 CDT)
    - Re: [AMBER] Installation issue Ashveen Seenauth (Tue Sep 22 2009 - 12:25:12 CDT)
    - Re: [AMBER] Installation issue Tom Joseph (Tue Sep 22 2009 - 12:41:51 CDT)
[AMBER] group distance restraint XIAOHUICANG (Tue Sep 22 2009 - 14:36:03 CDT)
[AMBER] Parameter Problem manoj singh (Tue Sep 22 2009 - 14:35:53 CDT)
[AMBER] Problem regarding Hbond analysis Abhishek Singh (Tue Sep 22 2009 - 14:43:50 CDT)
[AMBER] Parameter Problem manoj singh (Tue Sep 22 2009 - 14:46:59 CDT)
- Re: [AMBER] Parameter Problem FyD (Wed Sep 23 2009 - 03:28:49 CDT)
  - Re: [AMBER] Parameter Problem Manish Kumar (Wed Sep 23 2009 - 08:28:11 CDT)
Re: [AMBER] Problem regarding Hbond analysis Bill Ross (Tue Sep 22 2009 - 15:00:55 CDT)
[AMBER] parameter for manganese Yuqin Cai (Tue Sep 22 2009 - 17:48:41 CDT)
- Re: [AMBER] parameter for manganese Mahmoud A. A. Ibrahim (Thu Sep 24 2009 - 07:17:29 CDT)
[AMBER] apbs-amber Rilei Yu (Tue Sep 22 2009 - 17:58:40 CDT)
- Re: [AMBER] apbs-amber Robert Konecny (Tue Sep 22 2009 - 18:18:28 CDT)
  - Re: [AMBER] apbs-amber Rilei Yu (Tue Sep 22 2009 - 20:41:08 CDT)
[AMBER] solvent accessible surface area Ganesh Kamath (Wed Sep 23 2009 - 14:07:23 CDT)
- Re: [AMBER] solvent accessible surface area Carlos Simmerling (Wed Sep 23 2009 - 14:20:24 CDT)
  - Re: [AMBER] solvent accessible surface area Ganesh Kamath (Wed Sep 23 2009 - 14:26:33 CDT)
[AMBER] fatal "does not have a type" error in tleap for a protein-ligand complex Jeff Yeo (Wed Sep 23 2009 - 18:24:51 CDT)
- Re: [AMBER] fatal "does not have a type" error in tleap for a protein-ligand complex case (Thu Sep 24 2009 - 17:13:39 CDT)
[AMBER] Teragrid Beale, John (Thu Sep 24 2009 - 07:08:56 CDT)
- Re: [AMBER] Teragrid Carlos Simmerling (Thu Sep 24 2009 - 07:11:41 CDT)
[AMBER] CH3Hg+ parameters babak minoofar (Thu Sep 24 2009 - 07:08:12 CDT)
[AMBER] Ewald error estimated xuemeiwang1103 (Thu Sep 24 2009 - 22:01:02 CDT)
- Re: [AMBER] Ewald error estimated Qinghua Liao (Fri Sep 25 2009 - 02:48:14 CDT)
- Re: [AMBER] Ewald error estimated case (Fri Sep 25 2009 - 10:15:31 CDT)
  - Re: [AMBER] Ewald error estimated Robert Duke (Fri Sep 25 2009 - 10:50:18 CDT)
[AMBER] Ewald error estimated xuemeiwang1103 (Thu Sep 24 2009 - 22:01:05 CDT)
[AMBER] pmemd and internal dielectric Serguei Vassiliev (Fri Sep 25 2009 - 10:47:50 CDT)
- Re: [AMBER] pmemd and internal dielectric Robert Duke (Fri Sep 25 2009 - 11:07:06 CDT)
  - Re: [AMBER] pmemd and internal dielectric Adrian Roitberg (Fri Sep 25 2009 - 11:44:56 CDT)
  - Re: [AMBER] pmemd and internal dielectric Serguei Vassiliev (Fri Sep 25 2009 - 14:47:46 CDT)
[AMBER] Attaching a ligand to a protein residue. Kipras Redeckas (Fri Sep 25 2009 - 16:33:58 CDT)
- Re: [AMBER] Attaching a ligand to a protein residue. case (Sat Sep 26 2009 - 09:23:18 CDT)
  - Re: [AMBER] Attaching a ligand to a protein residue. Kipras Redeckas (Sun Sep 27 2009 - 05:23:42 CDT)
[AMBER] problem when doing mm/pbsa: bad atom type Br Baifan Wang (Sun Sep 27 2009 - 21:50:46 CDT)
- Re: [AMBER] problem when doing mm/pbsa: bad atom type Br Ray Luo (Sun Sep 27 2009 - 22:10:25 CDT)
  - Re: [AMBER] problem when doing mm/pbsa: bad atom type Br Baifan Wang (Mon Sep 28 2009 - 02:26:06 CDT)
[AMBER] How to obtain amber top and crd from pdb file with POPE lipids? decastro_at_physics.usyd.edu.au (Sun Sep 27 2009 - 23:52:20 CDT)
- Re: [AMBER] How to obtain amber top and crd from pdb file with POPE lipids? Hannes Loeffler (Mon Sep 28 2009 - 02:34:12 CDT)
[AMBER] Your help about ptraj in AmberTools!]] Rosina Noto (Mon Sep 28 2009 - 04:59:09 CDT)
[AMBER] trouble using iAPBS Oliver Kuhn (Mon Sep 28 2009 - 07:08:27 CDT)
- Re: [AMBER] trouble using iAPBS Robert Konecny (Mon Sep 28 2009 - 09:20:31 CDT)
- Re: [AMBER] trouble using iAPBS Oliver Kuhn (Thu Oct 01 2009 - 06:31:51 CDT)
  - Re: [AMBER] trouble using iAPBS Robert Konecny (Thu Oct 01 2009 - 12:27:42 CDT)
[AMBER] Gap in rst file Katrina Lexa (Mon Sep 28 2009 - 09:47:43 CDT)
[AMBER] LJ-partial charges and force field parameters for ethylene glycol and glycerol Ganesh Kamath (Mon Sep 28 2009 - 12:03:13 CDT)
- Re: [AMBER] LJ-partial charges and force field parameters for ethylene glycol and glycerol FyD (Mon Sep 28 2009 - 13:23:20 CDT)
[AMBER] partial charges in Amber force field Jihang Wang (Mon Sep 28 2009 - 12:52:28 CDT)
- Re: [AMBER] partial charges in Amber force field FyD (Mon Sep 28 2009 - 13:32:42 CDT)
[AMBER] why should one restrain the position of the counterions? Jose Borreguero (Mon Sep 28 2009 - 13:28:20 CDT)
[AMBER] Problem in compiling AMBER9 in parallel ! Pradipta Bandyopadhyay (Tue Sep 29 2009 - 08:04:47 CDT)
- Re: [AMBER] Problem in compiling AMBER9 in parallel ! Abhishek Banerjee (Tue Sep 29 2009 - 12:25:36 CDT)
- Re: [AMBER] Problem in compiling AMBER9 in parallel ! case (Tue Sep 29 2009 - 13:08:41 CDT)
[AMBER] Problem in test run Kshatresh Dutta Dubey (Tue Sep 29 2009 - 09:21:56 CDT)
- Re: [AMBER] Problem in test run Carlos Simmerling (Tue Sep 29 2009 - 09:26:38 CDT)
  - Re: [AMBER] Problem in test run Kshatresh Dutta Dubey (Tue Sep 29 2009 - 10:05:13 CDT)
- Re: [AMBER] Problem in test run case (Tue Sep 29 2009 - 11:50:19 CDT)
[AMBER] Zinc Sel Ercan (Tue Sep 29 2009 - 16:26:53 CDT)
- Re: [AMBER] Zinc Rubben Torella (Tue Sep 29 2009 - 16:31:31 CDT)
  - Re: [AMBER] Zinc Roman Osman (Tue Sep 29 2009 - 19:08:28 CDT)
[AMBER] Compiling Amber with gfortran-4.5.0 on a mac Ben Roberts (Tue Sep 29 2009 - 16:37:31 CDT)
- Re: [AMBER] Compiling Amber with gfortran-4.5.0 on a mac case (Fri Oct 02 2009 - 08:19:11 CDT)
  - Re: [AMBER] Compiling Amber with gfortran-4.5.0 on a mac Ben Roberts (Fri Oct 02 2009 - 09:20:47 CDT)
    - Re: [AMBER] Compiling Amber with gfortran-4.5.0 on a mac Mengjuei Hsieh (Tue Oct 06 2009 - 21:05:54 CDT)
[AMBER] MM_PBSA Zhongjie Liang (Tue Sep 29 2009 - 20:30:40 CDT)
[AMBER] too many missing parameters in frcmod for the prep of my ligand xueqin pang (Wed Sep 30 2009 - 04:21:31 CDT)
- Re: [AMBER] too many missing parameters in frcmod for the prep of my ligand FyD (Wed Sep 30 2009 - 05:30:32 CDT)
[AMBER] No restrt file xuemeiwang1103 (Wed Sep 30 2009 - 04:32:38 CDT)
- Re: [AMBER] No restrt file case (Wed Sep 30 2009 - 05:29:32 CDT)
  - Re:Re: [AMBER] No restrt file null (Wed Sep 30 2009 - 06:39:24 CDT)
    - Re: Re: [AMBER] No restrt file case (Wed Sep 30 2009 - 07:06:47 CDT)
[AMBER] xleap problem ! balaji nagarajan (Wed Sep 30 2009 - 13:40:58 CDT)
[AMBER] decomposing energies Beroza, Paul (Thu Oct 01 2009 - 11:15:07 CDT)
[AMBER] Environment Variables in Cygwin Don't Remain Wallace Kunin (Thu Oct 01 2009 - 11:54:29 CDT)
- Re: [AMBER] Environment Variables in Cygwin Don't Remain Jack Shultz (Thu Oct 01 2009 - 12:12:19 CDT)
Re: [AMBER] Environment Variables in Cygwin Don't Remain Bill Ross (Thu Oct 01 2009 - 13:57:43 CDT)
[AMBER] method used to determine partial charges? Paul Brandt (Thu Oct 01 2009 - 15:25:54 CDT)
- Re: [AMBER] method used to determine partial charges? Jihang Wang (Thu Oct 01 2009 - 15:36:31 CDT)
- Re: [AMBER] method used to determine partial charges? Bill Ross (Thu Oct 01 2009 - 16:19:29 CDT)
  - Re: [AMBER] method used to determine partial charges? Jihang Wang (Thu Oct 01 2009 - 16:28:45 CDT)
- Re: [AMBER] method used to determine partial charges? Bill Ross (Thu Oct 01 2009 - 17:18:01 CDT)
  - Re: [AMBER] method used to determine partial charges? Jihang Wang (Thu Oct 01 2009 - 17:26:24 CDT)
[AMBER] Dipole moment visualization. K.R. (Thu Oct 01 2009 - 16:37:29 CDT)
[AMBER] red problem James Moore (Thu Oct 01 2009 - 20:52:46 CDT)
- Re: [AMBER] red problem FyD (Thu Oct 01 2009 - 23:48:57 CDT)
[AMBER] Protein and charged surface rrd (Thu Oct 01 2009 - 22:49:18 CDT)
[AMBER] Different optimized structures with HF and B3LYP Sanghwa Han (Fri Oct 02 2009 - 02:50:10 CDT)
- Re: [AMBER] Different optimized structures with HF and B3LYP Karl Kirschner (Fri Oct 02 2009 - 03:07:08 CDT)
[AMBER] MM_PBSA decomposition pair question Rubben Torella (Fri Oct 02 2009 - 06:09:38 CDT)
[AMBER] minimization error balaji nagarajan (Fri Oct 02 2009 - 06:42:54 CDT)
- Re: [AMBER] minimization error case (Fri Oct 02 2009 - 07:00:52 CDT)
[AMBER] Missing X11 Libraries Wallace Kunin (Fri Oct 02 2009 - 11:43:59 CDT)
- [AMBER] Re: Missing X11 Libraries Wallace Kunin (Fri Oct 02 2009 - 11:55:34 CDT)
- Re: [AMBER] Missing X11 Libraries case (Fri Oct 02 2009 - 13:56:34 CDT)
  - Re: [AMBER] Missing X11 Libraries Wallace Kunin (Fri Oct 02 2009 - 14:57:49 CDT)
- Re: [AMBER] Missing X11 Libraries Bill Ross (Wed Oct 07 2009 - 17:28:34 CDT)
  - Re: [AMBER] Missing X11 Libraries Wallace Kunin (Thu Oct 08 2009 - 12:09:55 CDT)
- Re: [AMBER] Missing X11 Libraries Bill Ross (Thu Oct 08 2009 - 12:25:32 CDT)
- Re: [AMBER] Missing X11 Libraries Bill Ross (Fri Oct 09 2009 - 12:52:01 CDT)
  - Re: [AMBER] Missing X11 Libraries Wallace Kunin (Fri Oct 09 2009 - 14:20:00 CDT)
- Re: [AMBER] Missing X11 Libraries Bill Ross (Fri Oct 09 2009 - 19:24:47 CDT)
[AMBER] RMSD vs time and RMSD vs residues Olotu Odunayo (Fri Oct 02 2009 - 12:40:40 CDT)
- Re: [AMBER] RMSD vs time and RMSD vs residues Luis Gracia (Fri Oct 02 2009 - 13:07:10 CDT)
- Re: [AMBER] RMSD vs time and RMSD vs residues case (Fri Oct 02 2009 - 14:12:23 CDT)
- Re: [AMBER] RMSD vs time and RMSD vs residues Sally Pias (Fri Oct 02 2009 - 14:16:33 CDT)
[AMBER] probelm-APBS Rilei Yu (Sat Oct 03 2009 - 00:41:07 CDT)
- Re: [AMBER] probelm-APBS Robert Konecny (Sun Oct 04 2009 - 19:20:18 CDT)
  - Re: [AMBER] probelm-APBS Rilei Yu (Sun Oct 04 2009 - 19:51:10 CDT)
[AMBER] MMPBSA: No radius found for F Jeff Yeo (Sun Oct 04 2009 - 19:10:12 CDT)
[AMBER] TiO2 modeling stefano_elli_at_libero.it (Mon Oct 05 2009 - 11:00:59 CDT)
- [AMBER] new process_mdout.pl script???? Dean Cuebas (Mon Oct 05 2009 - 13:11:49 CDT)
  - RE: [AMBER] new process_mdout.pl script???? Ross Walker (Mon Oct 05 2009 - 13:38:17 CDT)
[AMBER] R.E.D.-III.3 tools release - q4md-forcefieldtools.org FyD (Sun Oct 04 2009 - 09:37:06 CDT)
[AMBER] pucker calculation for six member rings Ganesh Kamath (Mon Oct 05 2009 - 13:03:15 CDT)
[AMBER] MM/PBSA: NaN, Infinity and ************* in snapshot_com.all.out Jeff Yeo (Mon Oct 05 2009 - 18:22:53 CDT)
- Re: [AMBER] MM/PBSA: NaN, Infinity and ************* in snapshot_com.all.out Rubben Torella (Tue Oct 06 2009 - 02:56:18 CDT)
[AMBER] MM_PBSA: abnormal VDW interaction energy LIU Huanxiang (Mon Oct 05 2009 - 21:43:21 CDT)
- Re: [AMBER] MM_PBSA: abnormal VDW interaction energy steinbrt_at_rci.rutgers.edu (Tue Oct 06 2009 - 03:09:27 CDT)
  - Re: [AMBER] MM_PBSA: abnormal VDW interaction energy LIU Huanxiang (Tue Oct 06 2009 - 21:54:49 CDT)
[AMBER] mm_pbsa- Decomposition: bad atom type Antonija TomiÄ‡ (Tue Oct 06 2009 - 08:53:25 CDT)
[AMBER] Problem with memory in nmode analysis Alireza Shaneh (Tue Oct 06 2009 - 10:23:55 CDT)
[AMBER] using RESP program gunajyoti das (Wed Oct 07 2009 - 05:30:27 CDT)
- Re: [AMBER] using RESP program Ganesh Kamath (Wed Oct 07 2009 - 05:36:13 CDT)
  - Re: [AMBER] using RESP program FyD (Wed Oct 07 2009 - 15:04:38 CDT)
[AMBER] Re: Fw: Help required in Amber10 Installation Sudeep Narayan Banerjee (Wed Oct 07 2009 - 10:48:02 CDT)
- Re: [AMBER] Re: Fw: Help required in Amber10 Installation David Watson (Wed Oct 07 2009 - 10:53:26 CDT)
- Re: [AMBER] Re: Fw: Help required in Amber10 Installation Sudeep Narayan Banerjee (Thu Oct 15 2009 - 08:30:25 CDT)
  - Re: [AMBER] Re: Fw: Help required in Amber10 Installation case (Thu Oct 15 2009 - 08:45:42 CDT)
- Re: [AMBER] Re: Fw: Help required in Amber10 Installation Bill Ross (Thu Oct 15 2009 - 11:28:26 CDT)
Re: [AMBER] Re: Fw: Help required in Amber10 Installation Bill Ross (Wed Oct 07 2009 - 11:59:21 CDT)
- Re: [AMBER] Re: Fw: Help required in Amber10 Installation Chris Whittleston (Wed Oct 07 2009 - 12:48:18 CDT)
  - Re: [AMBER] Re: Fw: Help required in Amber10 Installation Sudeep Narayan Banerjee (Thu Oct 15 2009 - 07:11:01 CDT)
[AMBER] Combine and rename group of residues in xleap Lili Peng (Wed Oct 07 2009 - 16:49:23 CDT)
- Re: [AMBER] Combine and rename group of residues in xleap case (Fri Oct 09 2009 - 08:32:57 CDT)
[AMBER] The hydrophobic contribution Rilei Yu (Thu Oct 08 2009 - 00:48:32 CDT)
- Re: [AMBER] The hydrophobic contribution case (Thu Oct 08 2009 - 07:41:28 CDT)
[AMBER] Fwd: Group specification Pavan G (Thu Oct 08 2009 - 13:30:09 CDT)
- Re: [AMBER] Fwd: Group specification Carlos Simmerling (Thu Oct 08 2009 - 13:35:43 CDT)
Re: [AMBER] Fwd: Group specification Bill Ross (Thu Oct 08 2009 - 15:15:44 CDT)
- Re: [AMBER] Fwd: Group specification Bill Ross (Thu Oct 08 2009 - 15:22:54 CDT)
[AMBER] RE: VDW and TI for free energy Ross Walker (Thu Oct 08 2009 - 19:43:48 CDT)
[AMBER] ff03 parameter for GDP and GTP mmg8_at_ualberta.ca (Thu Oct 08 2009 - 20:05:18 CDT)
- Re: [AMBER] ff03 parameter for GDP and GTP FyD (Fri Oct 09 2009 - 05:37:40 CDT)
  - Re: [AMBER] ff03 parameter for GDP and GTP Carlos Simmerling (Fri Oct 09 2009 - 07:45:04 CDT)
  - Re: [AMBER] ff03 parameter for GDP and GTP mmg8_at_ualberta.ca (Fri Oct 09 2009 - 09:30:46 CDT)
    - Re: [AMBER] ff03 parameter for GDP and GTP FyD (Fri Oct 09 2009 - 15:38:08 CDT)
[AMBER] Some queries about pH simulation nicholus bhattacharjee (Thu Oct 08 2009 - 23:36:56 CDT)
- Re: [AMBER] Some queries about pH simulation Jason Swails (Fri Oct 09 2009 - 13:48:44 CDT)
  - Re: [AMBER] Some queries about pH simulation Carlos Simmerling (Fri Oct 09 2009 - 13:59:17 CDT)
[AMBER] DG improper torsion problem, two missing parameters Youn Kyeung Lee (Fri Oct 09 2009 - 02:02:03 CDT)
- Re: [AMBER] DG improper torsion problem, two missing parameters case (Fri Oct 09 2009 - 06:46:34 CDT)
[AMBER] Distance Replica Exchange Steve Seibold (Fri Oct 09 2009 - 08:18:44 CDT)
- Re: [AMBER] Distance Replica Exchange Carlos Simmerling (Fri Oct 09 2009 - 08:40:17 CDT)
  - RE: [AMBER] Distance Replica Exchange Steve Seibold (Fri Oct 09 2009 - 09:21:13 CDT)
Re: [AMBER] DG improper torsion problem, two missing parameters Bill Ross (Fri Oct 09 2009 - 12:25:30 CDT)
[AMBER] The -c option in Sander phani ghanakota (Fri Oct 09 2009 - 19:47:18 CDT)
- Re: [AMBER] The -c option in Sander case (Fri Oct 09 2009 - 20:54:05 CDT)
[AMBER] RE: VDW and TI for free energy Qicun Shi (Fri Oct 09 2009 - 21:00:08 CDT)
- Re: [AMBER] RE: VDW and TI for free energy steinbrt_at_rci.rutgers.edu (Sat Oct 10 2009 - 03:44:31 CDT)
  - Re: [AMBER] RE: VDW and TI for free energy Qicun Shi (Sat Oct 10 2009 - 23:05:20 CDT)
[AMBER] decomposition and calculation of entropy Qinghua Liao (Sat Oct 10 2009 - 01:13:49 CDT)
[AMBER] xleap-does not work Rilei Yu (Sat Oct 10 2009 - 03:30:06 CDT)
- Re: [AMBER] xleap-does not work case (Sat Oct 10 2009 - 07:27:01 CDT)
  - Re: [AMBER] xleap-does not work Rilei Yu (Sat Oct 10 2009 - 08:35:53 CDT)
[AMBER] A bug in LEaP ? FyD (Sun Oct 11 2009 - 07:08:37 CDT)
[AMBER] Energy-from-MM/PBSA-VS-experiment Rilei Yu (Sun Oct 11 2009 - 07:53:00 CDT)
- Re: [AMBER] Energy-from-MM/PBSA-VS-experiment Jason Swails (Sun Oct 11 2009 - 09:54:08 CDT)
  - Re: [AMBER] Energy-from-MM/PBSA-VS-experiment Rilei Yu (Sun Oct 11 2009 - 17:51:26 CDT)
[AMBER] S-S problem-in protein Rilei Yu (Sun Oct 11 2009 - 20:53:24 CDT)
- Re: [AMBER] S-S problem-in protein Jason Swails (Sun Oct 11 2009 - 21:15:10 CDT)
  - Re: [AMBER] S-S problem-in protein Jason Swails (Sun Oct 11 2009 - 23:24:51 CDT)
[AMBER] unit converter for force constants GÃœL ALTINBAÅž (Mon Oct 12 2009 - 07:22:00 CDT)
[AMBER] unit convertion for force constants GÃœL ALTINBAÅž (Mon Oct 12 2009 - 07:47:42 CDT)
- Re: [AMBER] unit convertion for force constants vhakkim boy (Mon Oct 12 2009 - 08:26:05 CDT)
[AMBER] OpenMP Ben Roberts (Mon Oct 12 2009 - 12:35:35 CDT)
- RE: [AMBER] OpenMP Ross Walker (Mon Oct 12 2009 - 13:29:45 CDT)
- Re: [AMBER] OpenMP michael (Tue Oct 13 2009 - 09:43:09 CDT)
[AMBER] Simulating transmembrane protein. Jayalakshmi Sridhar (Mon Oct 12 2009 - 13:42:11 CDT)
- Re: [AMBER] Simulating transmembrane protein. case (Mon Oct 12 2009 - 16:55:42 CDT)
[AMBER] Is iwrap mapping water molecules to my protein cavity? ben rodriguez (Mon Oct 12 2009 - 13:55:23 CDT)
- Re: [AMBER] Is iwrap mapping water molecules to my protein cavity? Carlos Simmerling (Mon Oct 12 2009 - 14:28:12 CDT)
Re: [AMBER] Simulating transmembrane protein. Bill Ross (Mon Oct 12 2009 - 14:04:36 CDT)
- Re: [AMBER] Simulating transmembrane protein. Jayalakshmi Sridhar (Mon Oct 12 2009 - 14:57:02 CDT)
- Re: [AMBER] Simulating transmembrane protein. Bill Ross (Mon Oct 12 2009 - 17:37:50 CDT)
Re: [AMBER] Is iwrap mapping water molecules to my protein cavity? Bill Ross (Mon Oct 12 2009 - 14:12:19 CDT)
[AMBER] Computing an Hessian matrix using NAB Brut Marie (Mon Oct 12 2009 - 17:12:44 CDT)
- Re: [AMBER] Computing an Hessian matrix using NAB case (Tue Oct 13 2009 - 07:13:42 CDT)
  - Re: [AMBER] Computing an Hessian matrix using NAB Brut Marie (Tue Oct 13 2009 - 13:56:19 CDT)
  - Re: [AMBER] Computing an Hessian matrix using NAB Brut Marie (Tue Oct 13 2009 - 14:00:53 CDT)
[AMBER] How to prepare the acetate ion file in leap? xuemeiwang1103 (Tue Oct 13 2009 - 02:05:57 CDT)
- Re: [AMBER] How to prepare the acetate ion file in leap? Balazs Jojart (Tue Oct 13 2009 - 02:36:03 CDT)
[AMBER] "Cannot open file ATOMTYPE.INF, exit" when using antechamber haifeng yuan (Tue Oct 13 2009 - 02:44:55 CDT)
- Re: [AMBER] "Cannot open file ATOMTYPE.INF, exit" when using antechamber case (Wed Oct 14 2009 - 06:37:35 CDT)
[AMBER] iAPBS - how to set the right grid dimensions Oliver Kuhn (Tue Oct 13 2009 - 03:36:27 CDT)
- Re: [AMBER] iAPBS - how to set the right grid dimensions Robert Konecny (Tue Oct 13 2009 - 09:42:12 CDT)
- Re: [AMBER] iAPBS - how to set the right grid dimensions Oliver Kuhn (Tue Oct 13 2009 - 10:17:06 CDT)
  - Re: [AMBER] iAPBS - how to set the right grid dimensions Robert Konecny (Tue Oct 13 2009 - 12:12:04 CDT)
- Re: [AMBER] iAPBS - how to set the right grid dimensions Oliver Kuhn (Wed Oct 14 2009 - 08:16:28 CDT)
  - Re: [AMBER] iAPBS - how to set the right grid dimensions Robert Konecny (Wed Oct 14 2009 - 08:21:07 CDT)
[AMBER] LES and NEB problem Rima Chaudhuri (Tue Oct 13 2009 - 14:35:37 CDT)
- Re: [AMBER] LES and NEB problem Carlos Simmerling (Wed Oct 14 2009 - 09:14:04 CDT)
  - Re: [AMBER] LES and NEB problem Rima Chaudhuri (Thu Oct 15 2009 - 11:50:08 CDT)
[AMBER] mean square displacment Nancy (Tue Oct 13 2009 - 18:59:15 CDT)
Re: [AMBER] mean square displacment Bill Ross (Tue Oct 13 2009 - 19:09:49 CDT)
[Amber]AMBER: MM_PBSA problems in AMBER10 He Hongqing (Tue Oct 13 2009 - 22:43:57 CDT)
- å›žå¤ï¼š [Amber]AMBER: MM_PBSA problems in AMBER10 Rilei Yu (Wed Oct 14 2009 - 00:47:02 CDT)
  - Re: å›žå¤ï¼š [Amber]AMBER: MM_PBSA problems in AMBER10 He Hongqing (Wed Oct 14 2009 - 02:32:25 CDT)
    - Re: å›žå¤ï¼š [Amber]AMBER: MM_PBSA problems in AMBER10 Rilei Yu (Wed Oct 14 2009 - 03:18:34 CDT)
- Re: [Amber]AMBER: MM_PBSA problems in AMBER10 Ray Luo (Wed Oct 14 2009 - 11:48:48 CDT)
[AMBER] How to add a hydrogen to the residue? xuemeiwang1103 (Tue Oct 13 2009 - 22:57:53 CDT)
- Re: [AMBER] How to add a hydrogen to the residue? case (Wed Oct 14 2009 - 06:51:08 CDT)
Re: Re: å›žå¤ï¼š [Amber]AMBER: MM_PBSA problemsin AMBER10 He Hongqing (Wed Oct 14 2009 - 03:39:33 CDT)
- Re: Re: å›žå¤ï¼š [Amber]AMBER: MM_PBSA problemsin AMBER10 Qinghua Liao (Wed Oct 14 2009 - 04:22:41 CDT)
  - Re: Re: Re: å›žå¤ï¼š [Amber]AMBER: MM_PBSA problemsin AMBER10 Bill Ross (Wed Oct 14 2009 - 11:56:41 CDT)
[AMBER] Add the hydrogen to the carboxyl of the GLU residue? xuemeiwang1103 (Wed Oct 14 2009 - 07:05:48 CDT)
- Re: [AMBER] Add the hydrogen to the carboxyl of the GLU residue? Andrew Purkiss-Trew (Wed Oct 14 2009 - 07:19:43 CDT)
- Re: [AMBER] Add the hydrogen to the carboxyl of the GLU residue? FyD (Wed Oct 14 2009 - 08:40:09 CDT)
  - Re: [AMBER] Add the hydrogen to the carboxyl of the GLU residue? Carlos Simmerling (Wed Oct 14 2009 - 08:49:00 CDT)
[AMBER] ptraj and prmtop Beale, John (Wed Oct 14 2009 - 07:46:11 CDT)
- Re: [AMBER] ptraj and prmtop Carlos Simmerling (Wed Oct 14 2009 - 08:41:04 CDT)
[AMBER] six member pucker calculation Ganesh Kamath (Wed Oct 14 2009 - 09:27:24 CDT)
[AMBER] nab normal mode analysis has imaginary frequencies Junmei Wang (Wed Oct 14 2009 - 11:05:06 CDT)
- Re: [AMBER] nab normal mode analysis has imaginary frequencies case (Wed Oct 14 2009 - 13:34:05 CDT)
- [AMBER] Re: nab normal mode analysis has imaginary frequencies Junmei Wang (Wed Dec 09 2009 - 17:34:28 CST)
  - Re: [AMBER] Re: nab normal mode analysis has imaginary frequencies case (Thu Dec 10 2009 - 08:46:20 CST)
[AMBER] installation of Amber on OSX Ramgopal Mettu (Wed Oct 14 2009 - 16:46:59 CDT)
- Re: [AMBER] installation of Amber on OSX David Watson (Wed Oct 14 2009 - 17:03:51 CDT)
- Re: [AMBER] installation of Amber on OSX case (Wed Oct 14 2009 - 17:10:04 CDT)
  - Re: [AMBER] installation of Amber on OSX Jason Swails (Wed Oct 14 2009 - 17:41:31 CDT)
[AMBER] Simulated annealing waleed zalloum (Thu Oct 15 2009 - 05:59:29 CDT)
- Re: [AMBER] Simulated annealing Carlos Simmerling (Thu Oct 15 2009 - 06:43:56 CDT)
[AMBER] part of the protein escaped from the water box qiaoyan (Thu Oct 15 2009 - 06:33:00 CDT)
- Re: [AMBER] part of the protein escaped from the water box Carlos Simmerling (Thu Oct 15 2009 - 06:39:40 CDT)
- Re: [AMBER] part of the protein escaped from the water box case (Thu Oct 15 2009 - 06:40:53 CDT)
- Re: [AMBER] part of the protein escaped from the water box Jason Swails (Thu Oct 15 2009 - 06:43:00 CDT)
[AMBER] Large File Support Beale, John (Thu Oct 15 2009 - 07:40:27 CDT)
- RE: [AMBER] Large File Support Ross Walker (Thu Oct 15 2009 - 13:14:01 CDT)
[AMBER] AMBER 11. Peter Winn (Thu Oct 15 2009 - 11:27:39 CDT)
- Re: [AMBER] AMBER 11. case (Thu Oct 15 2009 - 11:52:51 CDT)
[AMBER] B-factor Cristina Sisu (Thu Oct 15 2009 - 12:04:25 CDT)
- Re: [AMBER] B-factor Thomas Cheatham III (Fri Oct 16 2009 - 17:16:35 CDT)
  - Re: [AMBER] B-factor Cristina Sisu (Sat Oct 17 2009 - 05:58:34 CDT)
[AMBER] cross correlation analysis with ptraj Junmei Wang (Thu Oct 15 2009 - 11:49:29 CDT)
[AMBER] question with pucker in six member ring Ganesh Kamath (Thu Oct 15 2009 - 14:55:45 CDT)
- Re: [AMBER] question with pucker in six member ring Nicolas Sapay (Fri Oct 16 2009 - 10:04:24 CDT)
- Re: [AMBER] question with pucker in six member ring Thomas Cheatham III (Fri Oct 16 2009 - 13:23:05 CDT)
  - Re: [AMBER] question with pucker in six member ring Ganesh Kamath (Fri Oct 16 2009 - 13:36:41 CDT)
- Re: [AMBER] question with pucker in six member ring Bill Ross (Fri Oct 16 2009 - 13:43:56 CDT)
  - Re: [AMBER] question with pucker in six member ring Ganesh Kamath (Fri Oct 16 2009 - 14:31:31 CDT)
- Re: [AMBER] question with pucker in six member ring Bill Ross (Fri Oct 16 2009 - 14:48:04 CDT)
  - Re: [AMBER] question with pucker in six member ring Ganesh Kamath (Mon Oct 19 2009 - 12:42:17 CDT)
- Re: [AMBER] question with pucker in six member ring Bill Ross (Mon Oct 19 2009 - 12:54:03 CDT)
[AMBER] why is TAUTP scaled by "e" ? Jose Borreguero (Thu Oct 15 2009 - 15:49:18 CDT)
- RE: [AMBER] why is TAUTP scaled by "e" ? Ross Walker (Thu Oct 15 2009 - 17:08:52 CDT)
- Re: [AMBER] why is TAUTP scaled by "e" ? case (Fri Oct 16 2009 - 08:30:53 CDT)
  - Re: [AMBER] why is TAUTP scaled by "e" ? Jose Borreguero (Fri Oct 16 2009 - 14:13:42 CDT)
[AMBER] eigenvalues add up to more than trace of matrix Yaw Sing TAN (Thu Oct 15 2009 - 22:14:59 CDT)
- Re: [AMBER] eigenvalues add up to more than trace of matrix Jason Swails (Fri Oct 16 2009 - 08:29:13 CDT)
- Re: [AMBER] eigenvalues add up to more than trace of matrix Hannes Loeffler (Fri Oct 16 2009 - 08:50:50 CDT)
[AMBER] How to introduce the second protein molecule into simulation box? Siddharth Rastogi (Fri Oct 16 2009 - 02:00:03 CDT)
- Re: [AMBER] How to introduce the second protein molecule into simulation box? Jason Swails (Fri Oct 16 2009 - 08:15:57 CDT)
[AMBER] Re: AMBER: periodic bondary condition Markus Kaukonen (Fri Oct 16 2009 - 02:38:03 CDT)
- Re: [AMBER] Re: AMBER: periodic bondary condition case (Fri Oct 16 2009 - 08:13:49 CDT)
  - Re: [AMBER] Re: AMBER: periodic bondary condition Markus Kaukonen (Mon Oct 26 2009 - 03:14:48 CDT)
[AMBER] binding energy Simon Becker (Fri Oct 16 2009 - 04:28:39 CDT)
- Re: [AMBER] binding energy steinbrt_at_rci.rutgers.edu (Fri Oct 16 2009 - 06:27:24 CDT)
[AMBER] MMTSB cluster analysis versus ptraj cluster analysis Cenk \(Jenk\) Andac (Fri Oct 16 2009 - 07:19:24 CDT)
- Re: [AMBER] MMTSB cluster analysis versus ptraj cluster analysis Thomas Cheatham III (Fri Oct 16 2009 - 10:33:22 CDT)
  - Re: [AMBER] MMTSB cluster analysis versus ptraj cluster analysis Cenk \(Jenk\) Andac (Sat Oct 17 2009 - 02:02:20 CDT)
    - Re: [AMBER] MMTSB cluster analysis versus ptraj cluster analysis Jianyin Shao (Mon Oct 19 2009 - 13:16:47 CDT)
    - Re: [AMBER] MMTSB cluster analysis versus ptraj cluster analysis Cenk \(Jenk\) Andac (Mon Oct 19 2009 - 16:44:42 CDT)
[AMBER] AMBER FF and NAMD stefano_elli\_at_libero\.it (Fri Oct 16 2009 - 09:26:14 CDT)
- Re: [AMBER] AMBER FF and NAMD Hannes Loeffler (Fri Oct 16 2009 - 09:45:25 CDT)
- Re: [AMBER] AMBER FF and NAMD Nicolas Sapay (Fri Oct 16 2009 - 09:59:53 CDT)
- Re: [AMBER] AMBER FF and NAMD FyD (Fri Oct 16 2009 - 14:19:13 CDT)
[AMBER] Dihedral energy profile in a single molecule Frank X. Vázquez (Fri Oct 16 2009 - 09:55:53 CDT)
- Re: [AMBER] Dihedral energy profile in a single molecule Jason Swails (Fri Oct 16 2009 - 10:02:35 CDT)
[AMBER] RDC and alignment tensor Eliana Asciutto (Fri Oct 16 2009 - 15:21:34 CDT)
- Re: [AMBER] RDC and alignment tensor Thomas Cheatham III (Fri Oct 16 2009 - 15:45:25 CDT)
  - Re: [AMBER] RDC and alignment tensor Eliana Asciutto (Mon Oct 19 2009 - 11:50:31 CDT)
  - Re: [AMBER] RDC and alignment tensor Eliana Asciutto (Fri Oct 23 2009 - 14:19:00 CDT)
[AMBER] (no subject) Prakash Patodia (Sat Oct 17 2009 - 02:12:39 CDT)
- Re: [AMBER] (no subject) waleed zalloum (Wed Apr 29 2009 - 13:06:44 CDT)
[AMBER] How create PRMTOP and INCPRD for surface? rrd (Sat Oct 17 2009 - 21:40:02 CDT)
[AMBER] how to get hold of older versions of MKL ? Nahoum Anthony (Mon Oct 19 2009 - 03:59:57 CDT)
- Re: [AMBER] how to get hold of older versions of MKL ? Jason Swails (Mon Oct 19 2009 - 05:54:45 CDT)
- RE: [AMBER] how to get hold of older versions of MKL ? Ross Walker (Mon Oct 19 2009 - 11:58:54 CDT)
AW: [AMBER] Add the hydrogen to the carboxyl of the GLU residue? Aust, Susanne (Mon Oct 19 2009 - 04:01:27 CDT)
[AMBER] error message from iAPBS Oliver Kuhn (Mon Oct 19 2009 - 06:47:32 CDT)
[AMBER] Re: RDC and alignment tensor Eliana Asciutto (Mon Oct 19 2009 - 12:51:50 CDT)
- Re: [AMBER] Re: RDC and alignment tensor case (Mon Oct 19 2009 - 13:22:47 CDT)
[AMBER] Centering and reimaging with ptraj- stop rotating. ben rodriguez (Mon Oct 19 2009 - 22:00:26 CDT)
- Re: [AMBER] Centering and reimaging with ptraj- stop rotating. Thomas Cheatham (Mon Oct 19 2009 - 22:47:07 CDT)
- Re: [AMBER] Centering and reimaging with ptraj- stop rotating. Bill Ross (Tue Oct 20 2009 - 00:14:10 CDT)
[AMBER] Error: unable to find mopac charges in mopac.out Rilei Yu (Tue Oct 20 2009 - 00:34:34 CDT)
- RE: [AMBER] Error: unable to find mopac charges in mopac.out Ross Walker (Tue Oct 20 2009 - 00:50:17 CDT)
- RE: [AMBER] Error: unable to find mopac charges in mopac.out Rilei Yu (Tue Oct 20 2009 - 02:12:19 CDT)
  - Re: [AMBER] Error: unable to find mopac charges in mopac.out case (Tue Oct 20 2009 - 06:45:59 CDT)
[AMBER] How to create FF for diamond. rrd (Tue Oct 20 2009 - 01:16:07 CDT)
[AMBER] GAFF parameter stefano_elli\_at_libero\.it (Tue Oct 20 2009 - 08:26:26 CDT)
- Re: [AMBER] GAFF parameter Jason Swails (Tue Oct 20 2009 - 09:57:09 CDT)
- RE: [AMBER] GAFF parameter Ross Walker (Tue Oct 20 2009 - 13:50:18 CDT)
[AMBER] question with hbond in carnal Ganesh Kamath (Tue Oct 20 2009 - 08:58:36 CDT)
[AMBER] HBOND analysis Marcin Krol (Tue Oct 20 2009 - 10:42:35 CDT)
Re: [AMBER] question with hbond in carnal Bill Ross (Tue Oct 20 2009 - 11:32:56 CDT)
[AMBER] can I run EVB in other ensemble than NVE? Jose Borreguero (Tue Oct 20 2009 - 11:57:04 CDT)
- Re: [AMBER] can I run EVB in other ensemble than NVE? case (Tue Oct 20 2009 - 12:08:58 CDT)
[AMBER] man pages? Louis-Frédéric Feuillette (Tue Oct 20 2009 - 12:09:09 CDT)
- Re: [AMBER] man pages? Ben Roberts (Tue Oct 20 2009 - 12:33:16 CDT)
  - Re: [AMBER] man pages? Louis-Frédéric Feuillette (Tue Oct 20 2009 - 15:17:52 CDT)
    - Re: [AMBER] man pages? Jason Swails (Tue Oct 20 2009 - 16:28:56 CDT)
[AMBER] amber8 pmemd trajectory coordinates problem wong105_at_llnl.gov (Tue Oct 20 2009 - 19:32:24 CDT)
- Re: [AMBER] amber8 pmemd trajectory coordinates problem Thomas Cheatham (Tue Oct 20 2009 - 19:39:22 CDT)
  - Re: [AMBER] amber8 pmemd trajectory coordinates problem Sergio Wong (Tue Oct 20 2009 - 19:49:11 CDT)
    - Re: [AMBER] amber8 pmemd trajectory coordinates problem Robert Duke (Tue Oct 20 2009 - 20:03:37 CDT)
- Re: [AMBER] amber8 pmemd trajectory coordinates problem Robert Duke (Tue Oct 20 2009 - 20:15:56 CDT)
[AMBER] simulation blown up moitrayee_at_mbu.iisc.ernet.in (Tue Oct 20 2009 - 12:41:29 CDT)
- Re: [AMBER] simulation blown up Jason Swails (Tue Oct 20 2009 - 21:58:47 CDT)
- Re: [AMBER] simulation blown up Robert Duke (Tue Oct 20 2009 - 22:55:39 CDT)
[AMBER] Problem with running anal module in amber moitrayee_at_mbu.iisc.ernet.in (Wed Oct 21 2009 - 01:47:17 CDT)
[AMBER] "extra points" incompatibility with pmemd mousumi (Wed Oct 21 2009 - 02:57:51 CDT)
- Re: [AMBER] "extra points" incompatibility with pmemd Robert Duke (Wed Oct 21 2009 - 07:02:54 CDT)
  - Re: [AMBER] "extra points" incompatibility with pmemd Brent Krueger (Wed Oct 21 2009 - 07:28:58 CDT)
    - Re: [AMBER] "extra points" incompatibility with pmemd mousumi (Thu Oct 22 2009 - 00:20:48 CDT)
- Re: [AMBER] "extra points" incompatibility with pmemd case (Wed Oct 21 2009 - 07:22:28 CDT)
[AMBER] Can I use other ntb options in constant pH simulation nicholus bhattacharjee (Wed Oct 21 2009 - 04:26:43 CDT)
- Re: [AMBER] Can I use other ntb options in constant pH simulation Jason Swails (Wed Oct 21 2009 - 06:42:42 CDT)
[AMBER] Why the calculation ofen stop with the calculation process not end? xuemeiwang1103 (Wed Oct 21 2009 - 09:04:57 CDT)
[AMBER] xleap editing window icons inactive Jayalakshmi Sridhar (Wed Oct 21 2009 - 13:20:01 CDT)
- RE: [AMBER] xleap editing window icons inactive Niel Henriksen (Wed Oct 21 2009 - 13:21:54 CDT)
  - RE: [AMBER] xleap editing window icons inactive Jayalakshmi Sridhar (Wed Oct 21 2009 - 13:32:46 CDT)
[AMBER] Circular RNA topology file Kasprzak, Wojciech (NIH/NCI) [C] (Wed Oct 21 2009 - 13:26:04 CDT)
- Re: [AMBER] Circular RNA topology file case (Wed Oct 21 2009 - 14:06:17 CDT)
  - [AMBER] translate multiple residues Taufik Al-Sarraj (Wed Oct 21 2009 - 15:33:12 CDT)
    - Re: [AMBER] translate multiple residues Bill Ross (Wed Oct 21 2009 - 17:40:51 CDT)
  - Re: [AMBER] Circular RNA topology file Filip Lankas (Mon Oct 26 2009 - 05:13:46 CDT)
Re: [AMBER] translate multiple residues Bill Ross (Wed Oct 21 2009 - 15:53:20 CDT)
- Re: [AMBER] translate multiple residues Taufik Al-Sarraj (Wed Oct 21 2009 - 16:32:30 CDT)
[AMBER] Ptraj Segmentation Fault Katrina Hill (Wed Oct 21 2009 - 21:15:31 CDT)
[AMBER] too many undefined parameters in frcmod xueqin pang (Thu Oct 22 2009 - 03:52:57 CDT)
- Re: [AMBER] too many undefined parameters in frcmod FyD (Thu Oct 22 2009 - 04:37:46 CDT)
  - Re: [AMBER] too many undefined parameters in frcmod Jason Swails (Thu Oct 22 2009 - 06:59:55 CDT)
    - Re: [AMBER] too many undefined parameters in frcmod Junmei Wang (Mon Oct 26 2009 - 09:45:04 CDT)
    - Re: [AMBER] too many undefined parameters in frcmod xueqin pang (Thu Oct 29 2009 - 08:06:24 CDT)
  - [AMBER] Salt bridge time scale Mannan (Sun Oct 25 2009 - 20:57:20 CDT)
[AMBER] units of measures lorenzo (Thu Oct 22 2009 - 06:20:26 CDT)
- Re: [AMBER] units of measures case (Thu Oct 22 2009 - 07:42:11 CDT)
[AMBER] problem with minimization moitrayee_at_mbu.iisc.ernet.in (Thu Oct 22 2009 - 06:01:14 CDT)
[AMBER] [Fwd: problem with minimization] moitrayee_at_mbu.iisc.ernet.in (Thu Oct 22 2009 - 07:46:32 CDT)
[AMBER] parameters for O2 molecule Jeffrey (Thu Oct 22 2009 - 08:32:07 CDT)
- Re: [AMBER] parameters for O2 molecule Jason Swails (Thu Oct 22 2009 - 09:19:51 CDT)
  - Re: [AMBER] parameters for O2 molecule Jeffrey (Thu Oct 29 2009 - 08:01:44 CDT)
[AMBER] charges for heme-cys in p450 Jayalakshmi Sridhar (Thu Oct 22 2009 - 11:03:08 CDT)
- Re: [AMBER] charges for heme-cys in p450 FyD (Fri Oct 23 2009 - 05:57:43 CDT)
[AMBER] Unable to correctly identify element when running QM/MM in amber10 Jifeng Wang (Thu Oct 22 2009 - 11:20:30 CDT)
- RE: [AMBER] Unable to correctly identify element when running QM/MM in amber10 Ross Walker (Thu Oct 22 2009 - 14:03:40 CDT)
Re: [AMBER] [Fwd: problem with minimization] Bill Ross (Thu Oct 22 2009 - 11:49:45 CDT)
- Re: [AMBER] [Fwd: problem with minimization] moitrayee_at_mbu.iisc.ernet.in (Thu Oct 22 2009 - 13:53:11 CDT)
- Re: [AMBER] [Fwd: problem with minimization] Bill Ross (Fri Oct 23 2009 - 12:40:57 CDT)
[AMBER] XServe cluster Abdul Rehman Gani (Thu Oct 22 2009 - 14:14:36 CDT)
- Re: [AMBER] XServe cluster Jim Paugh (Thu Oct 22 2009 - 14:24:37 CDT)
  - Re: [AMBER] XServe cluster Abdul Rehman Gani (Thu Oct 22 2009 - 14:40:11 CDT)
    - Re: [AMBER] XServe cluster Jim Paugh (Thu Oct 22 2009 - 16:10:49 CDT)
- RE: [AMBER] XServe cluster Richard Owczarzy (Thu Oct 22 2009 - 15:02:24 CDT)
[AMBER] Question about distance restraint ? xuemeiwang1103 (Fri Oct 23 2009 - 05:07:47 CDT)
- Re: [AMBER] Question about distance restraint ? Carlos Simmerling (Fri Oct 23 2009 - 05:56:24 CDT)
[AMBER] amber parallel test fail Nahoum Anthony (Fri Oct 23 2009 - 05:20:45 CDT)
- Re: [AMBER] amber parallel test fail Jason Swails (Fri Oct 23 2009 - 06:58:19 CDT)
  - RE: [AMBER] amber parallel test fail Nahoum Anthony (Fri Oct 23 2009 - 10:12:40 CDT)
[AMBER] software to hydrate protein pockets Vlad Cojocaru (Fri Oct 23 2009 - 07:23:54 CDT)
- Re: [AMBER] software to hydrate protein pockets Alessandro Nascimento (Fri Oct 23 2009 - 07:50:05 CDT)
- Re: [AMBER] software to hydrate protein pockets Hannes Kopitz (Fri Oct 23 2009 - 08:11:26 CDT)
[AMBER] pmemd ifort problem Sel Ercan (Fri Oct 23 2009 - 09:57:59 CDT)
- Re: [AMBER] pmemd ifort problem Robert Duke (Fri Oct 23 2009 - 10:33:27 CDT)
[AMBER] inhibitor prepin not recognized in xleap Jayalakshmi Sridhar (Fri Oct 23 2009 - 10:56:40 CDT)
[AMBER] inhibitor prepin not recognized in xleap Jayalakshmi Sridhar (Fri Oct 23 2009 - 11:05:46 CDT)
[AMBER] xleap not reconizing inhibitor prepin Jayalakshmi Sridhar (Fri Oct 23 2009 - 11:21:07 CDT)
- Re: [AMBER] xleap not reconizing inhibitor prepin Junmei Wang (Mon Oct 26 2009 - 09:51:41 CDT)
Re: [AMBER] inhibitor prepin not recognized in xleap Bill Ross (Fri Oct 23 2009 - 13:32:03 CDT)
Re: [AMBER] xleap not reconizing inhibitor prepin Bill Ross (Fri Oct 23 2009 - 13:33:44 CDT)
[AMBER] the criterion of equilibrium qiaoyan (Fri Oct 23 2009 - 21:19:58 CDT)
[AMBER] resp_problem vhakkim boy (Sat Oct 24 2009 - 05:16:22 CDT)
- RE: [AMBER] resp_problem Ross Walker (Sat Oct 24 2009 - 17:39:01 CDT)
- Re: [AMBER] resp_problem FyD (Sun Oct 25 2009 - 01:12:31 CDT)
Re: [AMBER] the criterion of equilibrium Bill Ross (Sat Oct 24 2009 - 12:19:09 CDT)
- Re: [AMBER] the criterion of equilibrium Adrian Roitberg (Sat Oct 24 2009 - 13:22:25 CDT)
[AMBER] A bug in LEaP II ? FyD (Sun Oct 25 2009 - 07:58:36 CDT)
[AMBER] error in AMBer distance constraint xuemeiwang1103 (Sun Oct 25 2009 - 21:24:09 CDT)
- Re: [AMBER] error in AMBer distance constraint Carlos Simmerling (Sun Oct 25 2009 - 21:38:23 CDT)
  - Re:Re: [AMBER] error in AMBer distance constraint xuemeiwang1103 (Mon Oct 26 2009 - 02:35:08 CDT)
    - Re: Re: [AMBER] error in AMBer distance constraint Carlos Simmerling (Tue Oct 27 2009 - 06:28:22 CDT)
Re: [AMBER] error in AMBer distance constraint Bill Ross (Sun Oct 25 2009 - 22:03:19 CDT)
[AMBER] Preparing distance restraints Yunjie Zhao (Mon Oct 26 2009 - 03:44:58 CDT)
- Re: [AMBER] Preparing distance restraints case (Mon Oct 26 2009 - 16:26:26 CDT)
[AMBER] contradictive hydrogen bonds using ptraj Binbin Liu (Mon Oct 26 2009 - 11:42:20 CDT)
[AMBER] [amber10] atom groups used in torsion constrain Han Zheng (Mon Oct 26 2009 - 13:09:07 CDT)
[AMBER] PEMD Cristina Sisu (Mon Oct 26 2009 - 16:44:42 CDT)
- Re: [AMBER] PEMD Tom Joseph (Mon Oct 26 2009 - 18:03:26 CDT)
[AMBER] Possible bug in "com" group torsion angle constrain? Thanks! Han Zheng (Tue Oct 27 2009 - 12:28:16 CDT)
- RE: [AMBER] Possible bug in "com" group torsion angle constrain? Thanks! Seetin, Matthew (Tue Oct 27 2009 - 16:17:41 CDT)
  - Re: [AMBER] Possible bug in "com" group torsion angle constrain? Thanks! Han Zheng (Tue Oct 27 2009 - 17:47:20 CDT)
    - Re: [AMBER] Possible bug in "com" group torsion angle constrain? Thanks! Carlos Simmerling (Tue Oct 27 2009 - 18:22:43 CDT)
[AMBER] NMR restraint xuemeiwang1103 (Tue Oct 27 2009 - 21:31:39 CDT)
- Re: [AMBER] NMR restraint Sally Pias (Tue Oct 27 2009 - 23:32:33 CDT)
[AMBER] Simulated annealing Shaikh Abdul R S Ramaju (Wed Oct 28 2009 - 00:44:33 CDT)
- Re: [AMBER] Simulated annealing waleed zalloum (Fri Apr 24 2009 - 10:04:47 CDT)
  - Re: [AMBER] Simulated annealing Carlos Simmerling (Fri Apr 24 2009 - 10:44:02 CDT)
- Re: [AMBER] Simulated annealing Carlos Simmerling (Wed Oct 28 2009 - 05:51:41 CDT)
[AMBER] Conversion of Gaussian output file to mol2 megha bajaj (Wed Oct 28 2009 - 02:49:51 CDT)
[AMBER] Conversion of Gaussian output file into mol2 megha bajaj (Wed Oct 28 2009 - 03:00:35 CDT)
- Re: [AMBER] Conversion of Gaussian output file into mol2 Junmei Wang (Thu Oct 29 2009 - 10:45:27 CDT)
[AMBER] error in distance restraint xuemeiwang1103 (Wed Oct 28 2009 - 08:56:48 CDT)
- Re: [AMBER] error in distance restraint Adrian Roitberg (Wed Oct 28 2009 - 09:01:07 CDT)
  - [AMBER] vlimit Taufik Al-Sarraj (Wed Oct 28 2009 - 16:16:32 CDT)
- Re: [AMBER] error in distance restraint Carlos Simmerling (Wed Oct 28 2009 - 15:48:13 CDT)
  - Re:Re: [AMBER] error in distance restraint xuemeiwang1103 (Wed Oct 28 2009 - 22:43:55 CDT)
    - Re: Re: [AMBER] error in distance restraint Carlos Simmerling (Thu Oct 29 2009 - 05:20:13 CDT)
[AMBER] pairwise per-residue decomposition manoj singh (Wed Oct 28 2009 - 23:34:32 CDT)
- Re: [AMBER] pairwise per-residue decomposition Carlos Simmerling (Thu Oct 29 2009 - 05:20:55 CDT)
  - Re: [AMBER] pairwise per-residue decomposition manoj singh (Thu Oct 29 2009 - 12:32:38 CDT)
- Re: [AMBER] pairwise per-residue decomposition Tom Joseph (Thu Oct 29 2009 - 19:30:51 CDT)
- Re: [AMBER] pairwise per-residue decomposition Tom Joseph (Fri Oct 30 2009 - 00:15:40 CDT)
  - Re: [AMBER] pairwise per-residue decomposition manoj singh (Fri Oct 30 2009 - 00:46:22 CDT)
[AMBER] Thermodynamic Integration calculation on an artificial anion receptor Huifang (Wed Oct 28 2009 - 23:38:05 CDT)
- Re: [AMBER] Thermodynamic Integration calculation on an artificial anion receptor steinbrt_at_rci.rutgers.edu (Thu Oct 29 2009 - 05:35:24 CDT)
[AMBER] ligand exiting a protein cavity moitrayee_at_mbu.iisc.ernet.in (Thu Oct 29 2009 - 07:27:58 CDT)
[AMBER] [Fwd: ligand exiting a protein cavity] moitrayee_at_mbu.iisc.ernet.in (Thu Oct 29 2009 - 07:36:13 CDT)
- Re: [AMBER] [Fwd: ligand exiting a protein cavity] Kshatresh Dutta Dubey (Thu Oct 29 2009 - 09:44:28 CDT)
  - Re: [AMBER] [Fwd: ligand exiting a protein cavity] Jason Swails (Thu Oct 29 2009 - 10:17:40 CDT)
[AMBER] rms fit of mutant with respect to wild type structure Siddharth Rastogi (Thu Oct 29 2009 - 08:55:12 CDT)
- Re: [AMBER] rms fit of mutant with respect to wild type structure Carlos Simmerling (Thu Oct 29 2009 - 09:03:35 CDT)
[AMBER] Parallel sander & polarisability Thomas Taylor (Thu Oct 29 2009 - 11:19:14 CDT)
- RE: [AMBER] Parallel sander & polarisability Ross Walker (Thu Oct 29 2009 - 12:00:13 CDT)
- Re: [AMBER] Parallel sander & polarisability case (Thu Oct 29 2009 - 12:02:28 CDT)
[AMBER] Analyzing per-residue decomposition data manoj singh (Thu Oct 29 2009 - 15:18:45 CDT)
[AMBER] stacking clusters Shaikh Abdul R S Ramaju (Thu Oct 29 2009 - 21:44:59 CDT)
[AMBER] some queries on -states flag in constant pH simulation nicholus bhattacharjee (Thu Oct 29 2009 - 23:21:27 CDT)
- Re: [AMBER] some queries on -states flag in constant pH simulation Jason Swails (Fri Oct 30 2009 - 08:00:37 CDT)
  - Re: [AMBER] some queries on -states flag in constant pH simulation nicholus bhattacharjee (Sat Oct 31 2009 - 01:31:31 CDT)
    - Re: [AMBER] some queries on -states flag in constant pH simulation Jason Swails (Sat Oct 31 2009 - 07:28:22 CDT)
[AMBER] Ligand covalent bonds appear to be broken moitrayee_at_mbu.iisc.ernet.in (Fri Oct 30 2009 - 01:32:39 CDT)
- Re: [AMBER] Ligand covalent bonds appear to be broken Tom Joseph (Fri Oct 30 2009 - 06:53:44 CDT)
  - Re: [AMBER] Ligand covalent bonds appear to be broken Jason Swails (Fri Oct 30 2009 - 08:11:03 CDT)
    - Re: [AMBER] Ligand covalent bonds appear to be broken moitrayee_at_mbu.iisc.ernet.in (Fri Oct 30 2009 - 08:43:25 CDT)
- Re: [AMBER] Ligand covalent bonds appear to be broken Thomas Cheatham (Fri Oct 30 2009 - 10:48:07 CDT)
[AMBER] Is it the way to do simulation in vacuum nicholus bhattacharjee (Fri Oct 30 2009 - 05:18:45 CDT)
- Re: [AMBER] Is it the way to do simulation in vacuum Carlos Simmerling (Fri Oct 30 2009 - 05:21:49 CDT)
  - Re: [AMBER] Is it the way to do simulation in vacuum nicholus bhattacharjee (Fri Oct 30 2009 - 06:11:03 CDT)
[AMBER] SPC/E HOH angle Hemant Kumar (Fri Oct 30 2009 - 05:36:55 CDT)
- Re: [AMBER] SPC/E HOH angle case (Fri Oct 30 2009 - 07:51:41 CDT)
- Re: [AMBER] SPC/E HOH angle Carlos Simmerling (Fri Oct 30 2009 - 08:47:18 CDT)
[AMBER] RESP charges with -a and without -a flag Jio M (Fri Oct 30 2009 - 08:36:43 CDT)
- Re: [AMBER] RESP charges with -a and without -a flag Junmei Wang (Fri Oct 30 2009 - 11:49:00 CDT)
  - Re: [AMBER] RESP charges with -a and without -a flag Jio M (Sat Oct 31 2009 - 00:13:03 CDT)
[AMBER] Lennard Jones Potential A and B coefficients in Topology file Peter Schmidtke (Fri Oct 30 2009 - 13:32:32 CDT)
- Re: [AMBER] Lennard Jones Potential A and B coefficients in Topology file Tom Joseph (Fri Oct 30 2009 - 17:04:43 CDT)
  - Re: [AMBER] Lennard Jones Potential A and B coefficients in Topology file Peter Schmidtke (Fri Oct 30 2009 - 19:09:46 CDT)
[AMBER] Re: (files attached) RESP with -a and witout -a flag Jio M (Sat Oct 31 2009 - 00:17:55 CDT)
- [AMBER] Re: RESP with -a and witout -a flag Jio M (Sun Nov 01 2009 - 23:58:58 CST)
  - Re: [AMBER] Re: RESP with -a and witout -a flag Junmei Wang (Mon Nov 02 2009 - 10:48:48 CST)
    - [AMBER] Re: RESP with -a and witout -a flag Jio M (Wed Nov 04 2009 - 00:47:55 CST)
[AMBER] surface binding protein sadaf iqbal (Sat Oct 31 2009 - 00:28:22 CDT)
- Re: [AMBER] surface binding protein Jason Swails (Sat Oct 31 2009 - 07:35:44 CDT)
[AMBER] Gaussian log file error megha bajaj (Sat Oct 31 2009 - 08:10:22 CDT)
- Re: [AMBER] Gaussian log file error Ben Roberts (Mon Nov 02 2009 - 09:16:23 CST)
- Re: [AMBER] Gaussian log file error Junmei Wang (Mon Nov 02 2009 - 09:58:10 CST)
Re: [AMBER] Lennard Jones Potential A and B coefficients in Topology file Crowley, Michael (Sat Oct 31 2009 - 12:32:12 CDT)
[AMBER] Different results for different computers cyk5056 (Sat Oct 31 2009 - 14:39:59 CDT)
- Re: [AMBER] Different results for different computers manoj singh (Sat Oct 31 2009 - 14:47:36 CDT)
  - Re: [AMBER] Different results for different computers Jason Swails (Sat Oct 31 2009 - 14:57:34 CDT)
    - Re: [AMBER] Different results for different computers Robert Duke (Sat Oct 31 2009 - 17:56:28 CDT)
[AMBER] retinal lib file, params? Mark M Huntress (Sun Nov 01 2009 - 11:59:34 CST)
- Re: [AMBER] retinal lib file, params? Simon Becker (Mon Nov 02 2009 - 02:34:14 CST)
[AMBER] Is it taking too much time nicholus bhattacharjee (Mon Nov 02 2009 - 00:08:46 CST)
- Re: [AMBER] Is it taking too much time manoj singh (Mon Nov 02 2009 - 01:31:07 CST)
  - Re: [AMBER] Is it taking too much time nicholus bhattacharjee (Mon Nov 02 2009 - 02:37:28 CST)
[AMBER] MPI process terminated unexpectedly after cluster upgrade Dmitri Nilov (Mon Nov 02 2009 - 03:17:19 CST)
- Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade Jason Swails (Mon Nov 02 2009 - 06:15:19 CST)
  - Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade Dmitri Nilov (Mon Nov 02 2009 - 07:11:15 CST)
[AMBER] amber 10 test failures... peker milas (Mon Nov 02 2009 - 08:18:29 CST)
- RE: [AMBER] amber 10 test failures... Ross Walker (Mon Nov 02 2009 - 17:36:48 CST)
  - Re: [AMBER] amber 10 test failures... Mark Williamson (Mon Nov 02 2009 - 18:11:40 CST)
    - Re: [AMBER] amber 10 test failures... Jason Swails (Mon Nov 02 2009 - 18:19:43 CST)
    - Re: [AMBER] amber 10 test failures... peker milas (Tue Nov 03 2009 - 08:11:01 CST)
[AMBER] 60 giga output file .mdcrd file Silvia Carlotto (Mon Nov 02 2009 - 11:41:32 CST)
- Re: [AMBER] 60 giga output file .mdcrd file Peter Schmidtke (Mon Nov 02 2009 - 12:40:48 CST)
- RE: [AMBER] 60 giga output file .mdcrd file Ross Walker (Mon Nov 02 2009 - 17:36:48 CST)
  - Re: [AMBER] 60 giga output file .mdcrd file Silvia Carlotto (Tue Nov 03 2009 - 04:24:03 CST)
[AMBER] Is it possible to simulate transmembrane protein with GB model ? cgji (Mon Nov 02 2009 - 14:52:44 CST)
[AMBER] RE: question Ross Walker (Mon Nov 02 2009 - 17:36:48 CST)
- [AMBER] Re: question Marek Maly (Tue Nov 03 2009 - 14:22:16 CST)
- Re: [AMBER] RE: question rrd (Wed Nov 04 2009 - 20:52:04 CST)
  - Re: [AMBER] RE: question steinbrt_at_rci.rutgers.edu (Thu Nov 05 2009 - 02:12:47 CST)
    - Re: [AMBER] RE: question Marek Maly (Thu Nov 05 2009 - 07:28:03 CST)
    - Re: [AMBER] RE: question rrd (Thu Nov 05 2009 - 18:09:11 CST)
[AMBER] sander.APBS install problem Rilei Yu (Mon Nov 02 2009 - 19:58:30 CST)
- Re: [AMBER] sander.APBS install problem Robert Konecny (Mon Nov 02 2009 - 22:52:09 CST)
[AMBER] Phosphorylated Threonine Beale, John (Tue Nov 03 2009 - 10:31:09 CST)
- Re: [AMBER] Phosphorylated Threonine FyD (Tue Nov 03 2009 - 13:41:49 CST)
[AMBER] AMBER: segmentation fault when running parmchk Alexander Boncheff (Tue Nov 03 2009 - 13:41:55 CST)
- Re: [AMBER] AMBER: segmentation fault when running parmchk Jason Swails (Tue Nov 03 2009 - 14:22:10 CST)
  - Re: [AMBER] AMBER: segmentation fault when running parmchk Alexander Boncheff (Tue Nov 03 2009 - 16:29:00 CST)
- Re: [AMBER] AMBER: segmentation fault when running parmchk Bill Ross (Tue Nov 03 2009 - 17:15:00 CST)
- Re: [AMBER] AMBER: segmentation fault when running parmchk Bill Ross (Wed Nov 04 2009 - 12:39:32 CST)
- Re: [AMBER] AMBER: segmentation fault when running parmchk Junmei Wang (Wed Nov 04 2009 - 13:22:54 CST)
[AMBER] error in reading namelist cntrl Giuseppe De Marco (Tue Nov 03 2009 - 13:44:01 CST)
- RE: [AMBER] error in reading namelist cntrl Ross Walker (Tue Nov 03 2009 - 16:57:58 CST)
[AMBER] Antechamber and Parmchk problems cyk5056 (Tue Nov 03 2009 - 20:22:38 CST)
- Re: [AMBER] Antechamber and Parmchk problems case (Wed Nov 04 2009 - 09:26:03 CST)
  - Re: [AMBER] Antechamber and Parmchk problems Junmei Wang (Wed Nov 04 2009 - 13:21:25 CST)
- Re: Re: [AMBER] Antechamber and Parmchk problems cyk5056 (Wed Nov 04 2009 - 13:56:32 CST)
[AMBER] ambr parameter file creation and usage Donald Keidel (Tue Nov 03 2009 - 22:39:38 CST)
[AMBER] amber parameter file creation and usage Donald Keidel (Tue Nov 03 2009 - 22:47:36 CST)
- Re: [AMBER] amber parameter file creation and usage Jason Swails (Tue Nov 03 2009 - 23:29:30 CST)
  - Re: [AMBER] amber parameter file creation and usage Donald Keidel (Wed Nov 04 2009 - 11:53:23 CST)
[AMBER] errors on leap for a RNA+Adenine pdb structure zgong.hust (Wed Nov 04 2009 - 00:18:41 CST)
- Re: [AMBER] errors on leap for a RNA+Adenine pdb structure case (Wed Nov 04 2009 - 06:17:53 CST)
  - Re: Re: [AMBER] errors on leap for a RNA+Adenine pdb structure zgong.hust (Wed Nov 04 2009 - 06:59:20 CST)
[AMBER] total number of hydrogen bonds of the system as a function of time Markus Kaukonen (Wed Nov 04 2009 - 07:59:17 CST)
- Re: [AMBER] total number of hydrogen bonds of the system as a function of time Jason Swails (Wed Nov 04 2009 - 08:08:21 CST)
[AMBER] HB for each snapshot Marcin Krol (Wed Nov 04 2009 - 13:14:41 CST)
- Re: [AMBER] HB for each snapshot Jason Swails (Wed Nov 04 2009 - 13:35:07 CST)
- Re: [AMBER] HB for each snapshot Nicolas Sapay (Thu Nov 05 2009 - 02:30:51 CST)
[AMBER] Phosphothreonine Beale, John (Thu Nov 05 2009 - 07:03:58 CST)
- Re: [AMBER] Phosphothreonine Anselm Horn (Thu Nov 05 2009 - 07:17:59 CST)
[AMBER] Calculaiton stop ? xuemeiwang1103 (Thu Nov 05 2009 - 07:11:31 CST)
[AMBER] zeros in excluded atom list in topology file Peter Schmidtke (Thu Nov 05 2009 - 11:06:41 CST)
- Re: [AMBER] zeros in excluded atom list in topology file Carlos Simmerling (Thu Nov 05 2009 - 18:39:56 CST)
  - Re: [AMBER] zeros in excluded atom list in topology file Peter Schmidtke (Fri Nov 06 2009 - 02:54:57 CST)
- Re: [AMBER] zeros in excluded atom list in topology file case (Fri Nov 06 2009 - 16:44:04 CST)
  - Re: [AMBER] zeros in excluded atom list in topology file Peter Schmidtke (Fri Nov 06 2009 - 18:07:44 CST)
- Re: [AMBER] zeros in excluded atom list in topology file Bill Ross (Fri Nov 06 2009 - 18:09:39 CST)
[AMBER] Segmentation Fault Beale, John (Thu Nov 05 2009 - 12:04:52 CST)
- RE: [AMBER] Segmentation Fault Ross Walker (Thu Nov 05 2009 - 12:29:20 CST)
[AMBER] RESP using antechamber with Se atom Donald Keidel (Thu Nov 05 2009 - 13:21:37 CST)
- Re: [AMBER] RESP using antechamber with Se atom Junmei Wang (Thu Nov 05 2009 - 15:39:46 CST)
- Re: [AMBER] RESP using antechamber with Se atom subarna thakur (Thu Nov 05 2009 - 23:21:46 CST)
- Re: [AMBER] RESP using antechamber with Se atom Eric Pettersen (Fri Nov 06 2009 - 10:49:16 CST)
[AMBER] ff fitting ? Marek Maly (Thu Nov 05 2009 - 15:38:38 CST)
- Re: [AMBER] ff fitting ? case (Sun Nov 08 2009 - 11:42:42 CST)
  - Re: [AMBER] ff fitting ? Marek Maly (Mon Nov 09 2009 - 06:38:35 CST)
[AMBER] varying positional restraints with PMEMD Julian Garrec (Thu Nov 05 2009 - 18:43:35 CST)
- Re: [AMBER] varying positional restraints with PMEMD case (Sun Nov 08 2009 - 11:37:53 CST)
[AMBER] error in kclust of MMTB_tool set kureeckal ramesh (Fri Nov 06 2009 - 01:33:01 CST)
- [AMBER] -np not 2^x a problem w/ sander??? Dean Cuebas (Fri Nov 06 2009 - 13:27:48 CST)
  - RE: [AMBER] -np not 2^x a problem w/ sander??? Ross Walker (Fri Nov 06 2009 - 19:43:04 CST)
- [AMBER] -np not 2^x a problem w/ sander??? update Dean Cuebas (Fri Nov 06 2009 - 13:46:39 CST)
  - RE: [AMBER] -np not 2^x a problem w/ sander??? update Ross Walker (Sat Nov 07 2009 - 10:31:36 CST)
- [AMBER] ptraj script for H bond for protein (explicit ) kureeckal ramesh (Sat Nov 07 2009 - 01:38:29 CST)
[AMBER] amber9 compilation Myunggi Yi (Fri Nov 06 2009 - 09:10:03 CST)
- Re: [AMBER] amber9 compilation David Watson (Fri Nov 06 2009 - 09:19:31 CST)
  - Re: [AMBER] amber9 compilation Myunggi Yi (Fri Nov 06 2009 - 09:50:25 CST)
    - Re: [AMBER] amber9 compilation David Watson (Fri Nov 06 2009 - 10:16:58 CST)
[AMBER] amber 9 compilation Myunggi Yi (Fri Nov 06 2009 - 09:13:00 CST)
[AMBER] unable to find mopac charges in mopac.out Richard Tseng (Fri Nov 06 2009 - 19:14:20 CST)
- Re: [AMBER] unable to find mopac charges in mopac.out case (Sat Nov 07 2009 - 07:59:43 CST)
  - Re: [AMBER] unable to find mopac charges in mopac.out Richard Tseng (Mon Nov 09 2009 - 10:39:51 CST)
    - Re: [AMBER] unable to find mopac charges in mopac.out case (Mon Nov 09 2009 - 10:47:01 CST)
    - Re: [AMBER] unable to find mopac charges in mopac.out Richard Tseng (Mon Nov 09 2009 - 13:25:11 CST)
Re: [AMBER] unable to find mopac charges in mopac.out Bill Ross (Fri Nov 06 2009 - 19:22:22 CST)
[AMBER] Low frequency Raman spectra babak minoofar (Sat Nov 07 2009 - 06:53:37 CST)
- Re: [AMBER] Low frequency Raman spectra case (Sat Nov 07 2009 - 09:02:02 CST)
[AMBER] the problem of nucgen.dat liangchen88_at_ucla.edu (Sat Nov 07 2009 - 08:41:49 CST)
- Re: [AMBER] the problem of nucgen.dat case (Sat Nov 07 2009 - 08:51:57 CST)
  - Re: [AMBER] the problem of nucgen.dat liangchen88_at_ucla.edu (Sat Nov 07 2009 - 21:48:54 CST)
    - Re: [AMBER] the problem of nucgen.dat case (Sun Nov 08 2009 - 10:19:03 CST)
[AMBER] linux version for Amber10 liangchen88_at_ucla.edu (Sat Nov 07 2009 - 09:28:05 CST)
- Re: [AMBER] linux version for Amber10 Peter Schmidtke (Sat Nov 07 2009 - 09:58:18 CST)
[AMBER] linux version for Amber10 liangchen88_at_ucla.edu (Sat Nov 07 2009 - 09:28:05 CST)
[AMBER] build up solvate box Huikuan Chao (Sat Nov 07 2009 - 14:29:50 CST)
[AMBER] sleap fastbld error Oliver Kuhn (Sat Nov 07 2009 - 14:39:29 CST)
[AMBER] sleap fastbld error is not an error Oliver Kuhn (Sat Nov 07 2009 - 15:07:35 CST)
[AMBER] LJ parameters for HO and HW manoj singh (Sat Nov 07 2009 - 23:21:22 CST)
- Re: [AMBER] LJ parameters for HO and HW Jason Swails (Sat Nov 07 2009 - 23:50:03 CST)
  - Re: [AMBER] LJ parameters for HO and HW manoj singh (Sun Nov 08 2009 - 00:09:13 CST)
    - Re: [AMBER] LJ parameters for HO and HW Jason Swails (Sun Nov 08 2009 - 09:14:45 CST)
    - Re: [AMBER] LJ parameters for HO and HW steinbrt_at_rci.rutgers.edu (Mon Nov 09 2009 - 02:23:20 CST)
- Re: [AMBER] LJ parameters for HO and HW Bill Ross (Mon Nov 09 2009 - 11:29:40 CST)
[AMBER] solvent Jio M (Sun Nov 08 2009 - 08:12:34 CST)
[AMBER] MM_PBSA enquiries s. Bill (Sun Nov 08 2009 - 08:53:04 CST)
- Re: [AMBER] MM_PBSA enquiries manoj singh (Sun Nov 08 2009 - 09:21:12 CST)
[AMBER] pmemd failure Francesco Pietra (Sun Nov 08 2009 - 10:52:28 CST)
- Re: [AMBER] pmemd failure Robert Duke (Sun Nov 08 2009 - 11:00:52 CST)
  - Re: [AMBER] pmemd failure Francesco Pietra (Sun Nov 08 2009 - 13:08:53 CST)
[AMBER] Gly -> Ala mutation manoj singh (Sun Nov 08 2009 - 11:25:46 CST)
- Re: [AMBER] Gly -> Ala mutation Jason Swails (Sun Nov 08 2009 - 11:53:29 CST)
  - Re: [AMBER] Gly -> Ala mutation manoj singh (Sun Nov 08 2009 - 13:14:23 CST)
[AMBER] error in kclust of MMTB_tool set kureeckal ramesh (Sun Nov 08 2009 - 18:10:58 CST)
[AMBER] analyzeMatrix: cannot find a match in the matrixInfoStack Naser Alijabbari (Sun Nov 08 2009 - 19:43:56 CST)
[AMBER] conversion of kelvin to kcal/mol aneesh cna (Sun Nov 08 2009 - 23:08:33 CST)
- Re: [AMBER] conversion of kelvin to kcal/mol manoj singh (Sun Nov 08 2009 - 23:17:03 CST)
  - Re: [AMBER] conversion of kelvin to kcal/mol aneesh cna (Mon Nov 09 2009 - 00:56:36 CST)
[AMBER] sander.mpi. mdfil: Error unknown flag: sander Andrew Voronkov (Mon Nov 09 2009 - 06:24:17 CST)
- Re: [AMBER] sander.mpi. mdfil: Error unknown flag: sander case (Mon Nov 09 2009 - 07:17:23 CST)
[AMBER] Task is running on supercomputer without any output Andrew Voronkov (Mon Nov 09 2009 - 06:39:36 CST)
- Re: [AMBER] Task is running on supercomputer without any output michael bane (Mon Nov 09 2009 - 06:51:17 CST)
  - Re: [AMBER] Task is running on supercomputer without any output Andrew Voronkov (Thu Nov 12 2009 - 07:24:56 CST)
[AMBER] PCA analysis with ptraj Alessandro Contini (Mon Nov 09 2009 - 11:00:19 CST)
- RE: [AMBER] PCA analysis with ptraj hannes.loeffler_at_stfc.ac.uk (Tue Nov 10 2009 - 02:13:29 CST)
  - RE: [AMBER] PCA analysis with ptraj Alessandro Contini (Tue Nov 10 2009 - 06:03:48 CST)
[AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Wallace Kunin (Mon Nov 09 2009 - 13:14:25 CST)
- Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala David Watson (Mon Nov 09 2009 - 13:28:31 CST)
- Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala case (Mon Nov 09 2009 - 14:02:42 CST)
  - Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Mark Williamson (Mon Nov 09 2009 - 14:14:03 CST)
    - Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala case (Mon Nov 09 2009 - 14:41:59 CST)
  - Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Wallace Kunin (Mon Nov 09 2009 - 16:05:32 CST)
- Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Bill Ross (Wed Nov 11 2009 - 11:54:01 CST)
  - Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Wallace Kunin (Wed Nov 11 2009 - 16:04:28 CST)
[AMBER] Getting minimized .pdb file without non-polar hydrogens Francesco Pietra (Mon Nov 09 2009 - 13:31:40 CST)
[AMBER] rectangular box with PME problem Ivan Gladich (Mon Nov 09 2009 - 16:18:16 CST)
[AMBER] three trials to create topologies with sleap and tleap Oliver Kuhn (Tue Nov 10 2009 - 03:34:36 CST)
[AMBER] error in kclust of MMTB_tool set kureeckal ramesh (Tue Nov 10 2009 - 06:41:31 CST)
[AMBER] MMTSB tool set PDF kureeckal ramesh (Tue Nov 10 2009 - 08:02:39 CST)
[AMBER] matrixinfoStack Naser Alijabbari (Tue Nov 10 2009 - 08:45:12 CST)
[AMBER] error reading namelist cntrl Shaikh Abdul R S Ramaju (Wed Nov 11 2009 - 00:51:45 CST)
- Re: [AMBER] error reading namelist cntrl Jason Swails (Wed Nov 11 2009 - 08:01:42 CST)
[AMBER] coarse-grained MD Francesco Pietra (Wed Nov 11 2009 - 02:27:27 CST)
- [AMBER] Increase Temperature to 550 K Chih-Ying Lin (Wed Nov 11 2009 - 09:27:41 CST)
[AMBER] Creating new residue with tleap. rrd (Wed Nov 11 2009 - 05:02:23 CST)
- Re: [AMBER] Creating new residue with tleap. case (Wed Nov 11 2009 - 06:37:47 CST)
[AMBER] Lisp library for amber analysis? Eric Shamay (Wed Nov 11 2009 - 15:54:12 CST)
[AMBER] reg. GBA balaji nagarajan (Thu Nov 12 2009 - 06:06:30 CST)
- Re: [AMBER] reg. GBA case (Thu Nov 12 2009 - 07:02:43 CST)
[AMBER] MD snapshots of most probable protein conformations in Amber Andrew Voronkov (Thu Nov 12 2009 - 07:23:22 CST)
- Re: [AMBER] MD snapshots of most probable protein conformations in Amber Adrian Roitberg (Thu Nov 12 2009 - 07:30:53 CST)
  - Re: [AMBER] MD snapshots of most probable protein conformations in Amber Andrew Voronkov (Wed Nov 18 2009 - 07:09:52 CST)
[AMBER] MM_PBSA energy per residue Hemant Kumar (Thu Nov 12 2009 - 08:27:22 CST)
[AMBER] slope Jio M (Thu Nov 12 2009 - 13:28:02 CST)
[AMBER] R.E.D. resp error s. Bill (Thu Nov 12 2009 - 14:23:31 CST)
- Re: [AMBER] R.E.D. resp error FyD (Thu Nov 12 2009 - 23:36:44 CST)
[AMBER] R.E.D. too small charges Andrei Neamtu (Fri Nov 13 2009 - 02:57:04 CST)
- Re: [AMBER] R.E.D. too small charges FyD (Fri Nov 13 2009 - 07:06:51 CST)
[AMBER] enquiry regarding parameter file to be used bharat lakhani (Fri Nov 13 2009 - 07:35:30 CST)
- Re: [AMBER] enquiry regarding parameter file to be used Carlos Simmerling (Fri Nov 13 2009 - 07:41:50 CST)
  - Re: [AMBER] enquiry regarding parameter file to be used bharat lakhani (Fri Nov 13 2009 - 23:52:58 CST)
[AMBER] matrixInfoStack Naser Alijabbari (Fri Nov 13 2009 - 08:52:52 CST)
[AMBER] request sculiujl (Fri Nov 13 2009 - 20:59:22 CST)
[AMBER] the different RMSD? qiaoyan (Fri Nov 13 2009 - 21:37:36 CST)
- Re: [AMBER] the different RMSD? Thomas Cheatham (Fri Nov 13 2009 - 21:40:56 CST)
- Re: Re: [AMBER] the different RMSD? qiaoyan (Fri Nov 13 2009 - 22:16:27 CST)
  - Re: Re: [AMBER] the different RMSD? Thomas Cheatham (Sat Nov 14 2009 - 10:25:43 CST)
  - Re: Re: Re: [AMBER] the different RMSD? qiaoyan (Sat Nov 14 2009 - 20:02:53 CST)
[AMBER] is rst file the last structure? qiaoyan (Fri Nov 13 2009 - 22:52:40 CST)
- Re: [AMBER] is rst file the last structure? Jason Swails (Sat Nov 14 2009 - 11:18:22 CST)
  - Re: [AMBER] is rst file the last structure? case (Sun Nov 15 2009 - 08:33:16 CST)
[AMBER] Hydrogen bond analysis for protein dna complex using ptraj shamoon siddiqui (Sat Nov 14 2009 - 09:56:04 CST)
- Re: [AMBER] Hydrogen bond analysis for protein dna complex using ptraj Carlos Simmerling (Sat Nov 14 2009 - 10:00:39 CST)
  - Re: [AMBER] Hydrogen bond analysis for protein dna complex using ptraj shamoon siddiqui (Sat Nov 14 2009 - 10:19:04 CST)
    - Re: [AMBER] Hydrogen bond analysis for protein dna complex using ptraj Thomas Cheatham (Sat Nov 14 2009 - 11:06:15 CST)
[AMBER] How to split mdcrd files shamoon siddiqui (Sun Nov 15 2009 - 11:22:52 CST)
- Re: [AMBER] How to split mdcrd files Carlos Simmerling (Sun Nov 15 2009 - 11:28:06 CST)
  - Re: [AMBER] How to split mdcrd files Carlos Simmerling (Sun Nov 15 2009 - 11:56:48 CST)
- Re: [AMBER] How to split mdcrd files Jason Swails (Sun Nov 15 2009 - 11:35:24 CST)
- Re: [AMBER] How to split mdcrd files Thomas Cheatham (Sun Nov 15 2009 - 15:06:34 CST)
[AMBER] slope {no reply} Jio M (Sun Nov 15 2009 - 13:03:17 CST)
- Re: [AMBER] slope {no reply} Carlos Simmerling (Sun Nov 15 2009 - 13:07:02 CST)
  - Re: [AMBER] slope Jio M (Sun Nov 15 2009 - 22:42:52 CST)
- Re: [AMBER] slope {no reply} Bill Ross (Mon Nov 16 2009 - 11:48:22 CST)
  - Re: [AMBER] slope {no reply} Jio M (Mon Nov 16 2009 - 23:13:44 CST)
- Re: [AMBER] slope {no reply} Bill Ross (Tue Nov 17 2009 - 11:51:08 CST)
- Re: [AMBER] slope {no reply} Bill Ross (Tue Nov 17 2009 - 19:04:48 CST)
[AMBER] Etot positive Jio M (Sun Nov 15 2009 - 23:06:22 CST)
- Re: [AMBER] Etot positive Carlos Simmerling (Mon Nov 16 2009 - 05:13:55 CST)
- RE: [AMBER] Etot positive Ross Walker (Mon Nov 16 2009 - 20:50:02 CST)
[AMBER] Segmentation fault in antechamber albert albert (Mon Nov 16 2009 - 09:28:20 CST)
- Re: [AMBER] Segmentation fault in antechamber case (Mon Nov 16 2009 - 09:53:30 CST)
  - Re: [AMBER] Segmentation fault in antechamber albert albert (Mon Nov 16 2009 - 10:23:02 CST)
- Re: [AMBER] Segmentation fault in antechamber Scott Brozell (Mon Dec 14 2009 - 23:34:39 CST)
[AMBER] Installing AMBER 10 on Ubuntu 9.10 Karmic Koala Wallace Kunin (Mon Nov 16 2009 - 10:43:18 CST)
- Re: [AMBER] Installing AMBER 10 on Ubuntu 9.10 Karmic Koala Mark Williamson (Mon Nov 16 2009 - 11:37:18 CST)
  - Re: [AMBER] Installing AMBER 10 on Ubuntu 9.10 Karmic Koala Wallace Kunin (Mon Nov 16 2009 - 13:07:20 CST)
[AMBER] Re:Etot positive Jio M (Mon Nov 16 2009 - 22:59:26 CST)
[AMBER] compilation problem of amber9 sculiujl (Tue Nov 17 2009 - 01:03:22 CST)
- Re: [AMBER] compilation problem of amber9 Jason Swails (Tue Nov 17 2009 - 08:55:46 CST)
[AMBER] compilation problem of amber sculiujl (Tue Nov 17 2009 - 01:33:52 CST)
- Re: [AMBER] compilation problem of amber Jason Swails (Tue Nov 17 2009 - 08:51:42 CST)
[AMBER] which is the best intel complier for amber 10? jacky zhao (Tue Nov 17 2009 - 02:24:30 CST)
[AMBER] About zinc parameters ? xuemeiwang1103 (Tue Nov 17 2009 - 02:52:56 CST)
- Re: [AMBER] About zinc parameters ? steinbrt_at_rci.rutgers.edu (Tue Nov 17 2009 - 04:35:24 CST)
  - Re: [AMBER] About zinc parameters ? Sally Pias (Tue Nov 17 2009 - 11:38:29 CST)
- Re: [AMBER] About zinc parameters ? Jason Swails (Tue Nov 17 2009 - 09:17:23 CST)
[AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov (Tue Nov 17 2009 - 09:47:12 CST)
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) Jason Swails (Tue Nov 17 2009 - 09:57:41 CST)
  - Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov (Tue Nov 17 2009 - 10:34:33 CST)
    - Re: [AMBER] non standart residue library creation with tleap (Zn atom) Jason Swails (Tue Nov 17 2009 - 12:05:05 CST)
    - Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD (Tue Nov 17 2009 - 14:10:03 CST)
- RE: [AMBER] non standart residue library creation with tleap (Zn atom) intra\\sa175950 (Tue Nov 17 2009 - 10:18:38 CST)
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov (Wed Nov 18 2009 - 07:19:58 CST)
  - Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD (Wed Nov 18 2009 - 08:29:14 CST)
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov (Tue Nov 24 2009 - 02:40:42 CST)
  - Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD (Tue Nov 24 2009 - 03:26:37 CST)
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) Bill Ross (Tue Nov 24 2009 - 12:09:45 CST)
[AMBER] tleap maximum coordination exceeded Jack Shultz (Tue Nov 17 2009 - 10:52:20 CST)
- Re: [AMBER] tleap maximum coordination exceeded FyD (Tue Nov 17 2009 - 14:18:20 CST)
- Re: [AMBER] tleap maximum coordination exceeded case (Tue Nov 17 2009 - 14:24:09 CST)
  - Re: [AMBER] tleap maximum coordination exceeded Jack Shultz (Tue Nov 17 2009 - 19:51:38 CST)
    - Re: [AMBER] tleap maximum coordination exceeded Jack Shultz (Tue Nov 17 2009 - 21:05:41 CST)
    - Re: [AMBER] tleap maximum coordination exceeded case (Tue Nov 17 2009 - 22:45:55 CST)
[AMBER] combining parameter files of ligand and enzyme Amire-Brahimi Benjamin (Tue Nov 17 2009 - 16:31:32 CST)
- Re: [AMBER] combining parameter files of ligand and enzyme FyD (Wed Nov 18 2009 - 01:49:23 CST)
[AMBER] have a question jacky zhao (Tue Nov 17 2009 - 19:54:36 CST)
Re: [AMBER] have a question Bill Ross (Tue Nov 17 2009 - 20:02:45 CST)
[AMBER] the different RMSD? qiaoyan (Tue Nov 17 2009 - 20:47:42 CST)
- å›žå¤ï¼š [AMBER] the different RMSD? Rilei Yu (Tue Nov 17 2009 - 23:25:17 CST)
[AMBER] How to change the input matrix for "analyze matrix" instruction? cyk5056 (Tue Nov 17 2009 - 22:37:43 CST)
- Re:[AMBER] How to change the input matrix for "analyze matrix" instruction? ³ÂÒ»Ù© (Wed Nov 18 2009 - 10:18:51 CST)
[AMBER] Can I get an average trajectory? cyk5056 (Tue Nov 17 2009 - 22:46:25 CST)
- Re: [AMBER] Can I get an average trajectory? Carlos Simmerling (Wed Nov 18 2009 - 06:08:59 CST)
- Re: Re: [AMBER] Can I get an average trajectory? cyk5056 (Wed Nov 18 2009 - 10:02:38 CST)
[AMBER] GB and Atom Type Alexander Seifert (Wed Nov 18 2009 - 02:58:32 CST)
- Re: [AMBER] GB and Atom Type Sally Pias (Wed Nov 18 2009 - 23:11:27 CST)
[AMBER] Asking help for parallel installation of Amber9 nicholus bhattacharjee (Wed Nov 18 2009 - 06:27:03 CST)
- Re: [AMBER] Asking help for parallel installation of Amber9 David Watson (Wed Nov 18 2009 - 06:36:03 CST)
  - Re: [AMBER] Asking help for parallel installation of Amber9 nicholus bhattacharjee (Wed Nov 18 2009 - 07:00:36 CST)
    - Re: [AMBER] Asking help for parallel installation of Amber9 David Watson (Wed Nov 18 2009 - 07:23:17 CST)
[AMBER] read substrate into leap sculiujl (Wed Nov 18 2009 - 07:37:19 CST)
- Re: [AMBER] read substrate into leap Jason Swails (Wed Nov 18 2009 - 12:53:30 CST)
  - Re:Re: [AMBER] read substrate into leap sculiujl (Wed Nov 18 2009 - 19:12:13 CST)
    - Re: Re: [AMBER] read substrate into leap Jason Swails (Wed Nov 18 2009 - 19:35:37 CST)
  - Re:Re: [AMBER] read substrate into leap Bill Ross (Wed Nov 18 2009 - 19:59:33 CST)
[AMBER] about divcon Alan (Wed Nov 18 2009 - 10:24:51 CST)
- Re: [AMBER] about divcon case (Wed Nov 18 2009 - 10:53:16 CST)
  - Re: [AMBER] about divcon Alan (Wed Nov 18 2009 - 11:07:44 CST)
    - Re: [AMBER] about divcon Jason Swails (Wed Nov 18 2009 - 13:09:43 CST)
Re: [AMBER] Asking help for parallel installation of Amber9 Bill Ross (Wed Nov 18 2009 - 11:48:51 CST)
- Re: [AMBER] Asking help for parallel installation of Amber9 David Watson (Wed Nov 18 2009 - 12:04:38 CST)
[AMBER] Is the integral value from RDF the same as average number of atoms? Gustaf Olsson (go22bi_at_student.hik.se) (Wed Nov 18 2009 - 15:56:31 CST)
[AMBER] AmberTools 1.3 has a likely release date? Alan (Thu Nov 19 2009 - 12:15:30 CST)
- Re: [AMBER] AmberTools 1.3 has a likely release date? case (Fri Nov 20 2009 - 08:50:23 CST)
[AMBER] implicit_run_error balaji nagarajan (Thu Nov 19 2009 - 12:37:21 CST)
- Re: [AMBER] implicit_run_error case (Fri Nov 20 2009 - 08:53:31 CST)
[AMBER] errors on leap for a RNA + Non-Standard molecule pdb structure Yunjie Zhao (Thu Nov 19 2009 - 22:37:34 CST)
[AMBER] rmsd Taufik Al-Sarraj (Fri Nov 20 2009 - 10:32:24 CST)
- Re: [AMBER] rmsd Thomas Cheatham (Sat Nov 21 2009 - 15:44:41 CST)
  - Re: [AMBER] rmsd Taufik Al-Sarraj (Mon Nov 23 2009 - 13:24:49 CST)
[AMBER] standard way to upload a lipid bilayer Syed Kashif Zafar (Sat Nov 21 2009 - 05:40:08 CST)
- Re: [AMBER] standard way to upload a lipid bilayer David Watson (Sat Nov 21 2009 - 07:06:29 CST)
[AMBER] looking for parameters for DHFR substrates and inhibitors... Sidney Elmer (Sat Nov 21 2009 - 22:47:50 CST)
[AMBER] NAD - mmpbsa Urszula Uciechowska (Sun Nov 22 2009 - 05:02:22 CST)
[AMBER] Polarizable simulation of the slab Jan Heyda (Sun Nov 22 2009 - 07:13:16 CST)
[AMBER] Fortran error in standard simulation Oliver Kuhn (Mon Nov 23 2009 - 03:26:30 CST)
- RE: [AMBER] Fortran error in standard simulation Ross Walker (Tue Nov 24 2009 - 10:21:33 CST)
[AMBER] Fortran error in standard simulation 2 Oliver Kuhn (Mon Nov 23 2009 - 03:34:21 CST)
[AMBER] Fortran error in standard simulation 3 Oliver Kuhn (Mon Nov 23 2009 - 03:47:44 CST)
[AMBER] matrixInfoStack Naser Alijabbari (Mon Nov 23 2009 - 08:42:43 CST)
[AMBER] hbond analysis by ptraj- segmentation fault Jayalakshmi Sridhar (Mon Nov 23 2009 - 09:51:00 CST)
- Re: [AMBER] hbond analysis by ptraj- segmentation fault Daniel Roe (Mon Nov 23 2009 - 11:42:49 CST)
- Re: [AMBER] hbond analysis by ptraj- segmentation fault Daniel Roe (Mon Nov 23 2009 - 11:49:23 CST)
  - Re: [AMBER] hbond analysis by ptraj- segmentation fault Jayalakshmi Sridhar (Mon Nov 23 2009 - 12:36:25 CST)
[AMBER] Regarding Urey-Bradley term in amber calculation aneesh cna (Tue Nov 24 2009 - 00:48:04 CST)
- Re: [AMBER] Regarding Urey-Bradley term in amber calculation Jason Swails (Tue Nov 24 2009 - 06:48:31 CST)
- RE: [AMBER] Regarding Urey-Bradley term in amber calculation Ross Walker (Tue Nov 24 2009 - 10:36:49 CST)
[AMBER] How to get total energy of asystem gunajyoti das (Tue Nov 24 2009 - 03:14:06 CST)
- Re: [AMBER] How to get total energy of asystem steinbrt_at_rci.rutgers.edu (Tue Nov 24 2009 - 03:43:06 CST)
- Re: [AMBER] How to get total energy of asystem case (Tue Nov 24 2009 - 06:36:30 CST)
[AMBER] Hbond analysis output giving no hbonds Jayalakshmi Sridhar (Tue Nov 24 2009 - 10:32:41 CST)
- RE: [AMBER] Hbond analysis output giving no hbonds Thomas Cheatham (Tue Nov 24 2009 - 10:58:27 CST)
  - RE: [AMBER] Hbond analysis output giving no hbonds Jayalakshmi Sridhar (Tue Nov 24 2009 - 11:52:47 CST)
[AMBER] trouble with antechamber Jennifer L. Muzyka (Tue Nov 24 2009 - 14:13:46 CST)
- Re: [AMBER] trouble with antechamber case (Tue Nov 24 2009 - 14:41:24 CST)
  - RE: [AMBER] trouble with antechamber Jennifer L. Muzyka (Mon Nov 30 2009 - 08:39:15 CST)
    - Re: [AMBER] trouble with antechamber case (Mon Nov 30 2009 - 08:57:26 CST)
    - RE: [AMBER] trouble with antechamber Jennifer L. Muzyka (Tue Dec 01 2009 - 09:10:40 CST)
[AMBER] how to use amber to verify the reason for difference in affinity Josmar R. da Rocha (Tue Nov 24 2009 - 16:01:34 CST)
- Re: [AMBER] how to use amber to verify the reason for difference in affinity case (Sun Nov 29 2009 - 20:55:38 CST)
[AMBER] check MAXPR in locmem.f error on minimization Jodi Hadden (Tue Nov 24 2009 - 17:46:03 CST)
- Re: [AMBER] check MAXPR in locmem.f error on minimization case (Wed Nov 25 2009 - 07:29:41 CST)
  - Re: [AMBER] check MAXPR in locmem.f error on minimization Jodi Hadden (Wed Nov 25 2009 - 12:29:51 CST)
    - Re: [AMBER] check MAXPR in locmem.f error on minimization Jason Swails (Wed Nov 25 2009 - 12:50:43 CST)
    - Re: [AMBER] check MAXPR in locmem.f error on minimization Robert Duke (Fri Nov 27 2009 - 08:44:36 CST)
[AMBER] MM-PBSA NMODE Zhongjie Liang (Tue Nov 24 2009 - 21:12:38 CST)
- Re: [AMBER] MM-PBSA NMODE case (Wed Nov 25 2009 - 07:31:28 CST)
[AMBER] i-APBS and apbs Rilei Yu (Tue Nov 24 2009 - 23:14:18 CST)
- Re: [AMBER] i-APBS and apbs Robert Konecny (Tue Nov 24 2009 - 23:33:37 CST)
- Re: [AMBER] i-APBS and apbs Jason Swails (Tue Nov 24 2009 - 23:33:31 CST)
- Re: [AMBER] i-APBS and apbs Rilei Yu (Wed Nov 25 2009 - 05:14:15 CST)
[AMBER] Not able to compile pmemd with openmpi in Amber9 Kito (Wed Nov 25 2009 - 00:39:42 CST)
- Re: [AMBER] Not able to compile pmemd with openmpi in Amber9 Jason Swails (Wed Nov 25 2009 - 01:06:14 CST)
- Re: [AMBER] Not able to compile pmemd with openmpi in Amber9 Kito (Wed Nov 25 2009 - 01:11:00 CST)
  - Re: Re: [AMBER] Not able to compile pmemd with openmpi in Amber9 Kito (Wed Nov 25 2009 - 01:50:25 CST)
[AMBER] MM-PB/GBSA NMODE Zhongjie Liang (Wed Nov 25 2009 - 00:50:50 CST)
[AMBER] heme (united-atom) Simon Becker (Wed Nov 25 2009 - 10:30:51 CST)
- Re: [AMBER] heme (united-atom) case (Wed Nov 25 2009 - 10:39:10 CST)
  - Re: [AMBER] heme (united-atom) Simon Becker (Thu Nov 26 2009 - 08:34:59 CST)
    - Re: [AMBER] heme (united-atom) case (Mon Nov 30 2009 - 07:28:05 CST)
[AMBER] Verlet update time in explicit water Replica Exchange MD Da-Wei Li (Wed Nov 25 2009 - 11:05:55 CST)
- Re: [AMBER] Verlet update time in explicit water Replica Exchange MD Carlos Simmerling (Wed Nov 25 2009 - 11:10:56 CST)
  - Re: [AMBER] Verlet update time in explicit water Replica Exchange MD Da-Wei Li (Wed Nov 25 2009 - 11:14:17 CST)
- [AMBER] Re: Verlet update time in explicit water Replica Exchange MD Da-Wei Li (Wed Nov 25 2009 - 11:12:23 CST)
[AMBER] difference between two inputs Jio M (Thu Nov 26 2009 - 00:32:12 CST)
- Re: [AMBER] difference between two inputs case (Fri Nov 27 2009 - 08:59:01 CST)
[AMBER] rings getting planar Jio M (Thu Nov 26 2009 - 03:33:09 CST)
- Re: [AMBER] rings getting planar Jio M (Thu Nov 26 2009 - 08:40:34 CST)
- Re: [AMBER] rings getting planar case (Thu Nov 26 2009 - 09:07:43 CST)
[AMBER] ligand parameterization Nahoum Anthony (Thu Nov 26 2009 - 04:49:51 CST)
- Re: [AMBER] ligand parameterization case (Thu Nov 26 2009 - 09:09:05 CST)
  - Re: [AMBER] ligand parameterization Jason Swails (Thu Nov 26 2009 - 09:47:58 CST)
[AMBER] Atomic radii assignment for WAT molecules DIMAS SUAREZ RODRIGUEZ (Thu Nov 26 2009 - 10:43:33 CST)
- Re: [AMBER] Atomic radii assignment for WAT molecules Ray Luo (Sat Nov 28 2009 - 12:13:42 CST)
[AMBER] Polarizable simulation of the slab Jan Heyda (Thu Nov 26 2009 - 12:20:52 CST)
- Re: [AMBER] Polarizable simulation of the slab case (Fri Nov 27 2009 - 08:24:41 CST)
  - Re: [AMBER] Polarizable simulation of the slab Jan Heyda (Fri Nov 27 2009 - 08:53:57 CST)
[AMBER] MM_PBSA error Jagdeesh C (Thu Nov 26 2009 - 22:28:44 CST)
- [AMBER] Re: MM_PBSA error Jagdeesh C (Fri Nov 27 2009 - 03:20:27 CST)
  - Re: [AMBER] Re: MM_PBSA error Mengjuei Hsieh (Fri Nov 27 2009 - 03:39:54 CST)
    - Re: [AMBER] Re: MM_PBSA error Jagdeesh C (Fri Nov 27 2009 - 04:13:36 CST)
    - Re: [AMBER] Re: MM_PBSA error Ray Luo (Sat Nov 28 2009 - 12:07:26 CST)
[AMBER] Regarding rigid bond aneesh cna (Fri Nov 27 2009 - 11:29:15 CST)
- Re: [AMBER] Regarding rigid bond Carlos Simmerling (Fri Nov 27 2009 - 12:24:35 CST)
  - Re: [AMBER] Regarding rigid bond aneesh cna (Mon Nov 30 2009 - 23:35:03 CST)
- Re: [AMBER] Regarding rigid bond Bill Ross (Tue Dec 01 2009 - 11:37:27 CST)
  - Re: [AMBER] Regarding rigid bond Adrian Roitberg (Tue Dec 01 2009 - 11:40:30 CST)
- Re: [AMBER] Regarding rigid bond Bill Ross (Tue Dec 01 2009 - 11:41:44 CST)
  - Re: [AMBER] Regarding rigid bond aneesh cna (Tue Dec 01 2009 - 23:17:46 CST)
- Re: [AMBER] Regarding rigid bond Bill Ross (Wed Dec 02 2009 - 11:20:52 CST)
[AMBER] LYS-ASP s. Bill (Fri Nov 27 2009 - 15:47:28 CST)
- Re: [AMBER] LYS-ASP Jason Swails (Fri Nov 27 2009 - 19:25:33 CST)
- Re: [AMBER] LYS-ASP case (Fri Nov 27 2009 - 21:08:58 CST)
[AMBER] where to get leaprc.ff99sb? Jack Shultz (Sat Nov 28 2009 - 18:20:03 CST)
- Re: [AMBER] where to get leaprc.ff99sb? Jason Swails (Sat Nov 28 2009 - 19:39:20 CST)
  - Re: [AMBER] where to get leaprc.ff99sb? Jack Shultz (Sat Nov 28 2009 - 21:19:33 CST)
    - Re: [AMBER] where to get leaprc.ff99sb? Jason Swails (Sat Nov 28 2009 - 21:51:39 CST)
[AMBER] Scripting tleap Jack Shultz (Sat Nov 28 2009 - 21:42:00 CST)
- Re: [AMBER] Scripting tleap Tom Joseph (Sat Nov 28 2009 - 21:45:40 CST)
  - Re: [AMBER] Scripting tleap Jack Shultz (Sat Nov 28 2009 - 21:54:25 CST)
[AMBER] How to compile and recompile ptraj? cyk5056 (Sun Nov 29 2009 - 16:06:55 CST)
- [AMBER] Re: How to compile and recompile ptraj? cyk5056 (Sun Nov 29 2009 - 16:53:37 CST)
  - Re: [AMBER] Re: How to compile and recompile ptraj? case (Sun Nov 29 2009 - 19:41:24 CST)
[AMBER] how to use GLYCAM04 for carbonhydrate in amber9? sculiujl (Sun Nov 29 2009 - 21:39:08 CST)
- Re: [AMBER] how to use GLYCAM04 for carbonhydrate in amber9? Karl Kirschner (Mon Nov 30 2009 - 02:53:27 CST)
[AMBER] reagarding Dihedral PCA jani sahil (Mon Nov 30 2009 - 00:24:28 CST)
[AMBER] regarding Dihedral PCA jani sahil (Mon Nov 30 2009 - 00:25:08 CST)
[AMBER] distance-dependent dielectric constant minimization Rilei Yu (Mon Nov 30 2009 - 01:02:32 CST)
- Re: [AMBER] distance-dependent dielectric constant minimization case (Mon Nov 30 2009 - 07:02:11 CST)
  - Re: [AMBER] distance-dependent dielectric constant minimization Rilei Yu (Mon Nov 30 2009 - 23:31:58 CST)
- Re: [AMBER] distance-dependent dielectric constant minimization Bill Ross (Sat Dec 05 2009 - 11:30:09 CST)
[AMBER] trajout problem Anna Reymer (Mon Nov 30 2009 - 06:03:38 CST)
- Re: [AMBER] trajout problem Carlos Simmerling (Mon Nov 30 2009 - 06:09:05 CST)
  - RE: [AMBER] trajout problem Anna Reymer (Mon Nov 30 2009 - 06:58:39 CST)
- Re: [AMBER] trajout problem Sally Pias (Mon Nov 30 2009 - 13:01:52 CST)
[AMBER] problem with FAD in tleap M. Shahid (Mon Nov 30 2009 - 06:17:09 CST)
- Re: [AMBER] problem with FAD in tleap FyD (Mon Nov 30 2009 - 07:02:59 CST)
  - Re: [AMBER] problem with FAD in tleap M. Shahid (Mon Nov 30 2009 - 09:54:26 CST)
- Re: [AMBER] problem with FAD in tleap case (Mon Nov 30 2009 - 07:26:37 CST)
[AMBER] Output Does Not Match in Tutorial B1 Wallace Kunin (Mon Nov 30 2009 - 12:38:07 CST)
- Re: [AMBER] Output Does Not Match in Tutorial B1 case (Mon Nov 30 2009 - 13:01:20 CST)
  - Re: [AMBER] Output Does Not Match in Tutorial B1 Wallace Kunin (Mon Nov 30 2009 - 13:11:02 CST)
Re: [AMBER] Output Does Not Match in Tutorial B1 Bill Ross (Mon Nov 30 2009 - 13:03:19 CST)
[AMBER] fillratio Qinghua Liao (Mon Nov 30 2009 - 20:38:34 CST)
- Re: [AMBER] fillratio Ray Luo (Mon Nov 30 2009 - 21:30:50 CST)
  - Re: [AMBER] fillratio Qinghua Liao (Mon Nov 30 2009 - 23:59:05 CST)
[AMBER] ptraj utility Neha Bharat Gajaria (Tue Dec 01 2009 - 02:30:07 CST)
- Re: [AMBER] ptraj utility Daniel Roe (Tue Dec 01 2009 - 06:45:19 CST)
  - Re: [AMBER] ptraj utility Carlos Simmerling (Tue Dec 01 2009 - 06:48:27 CST)
- Re: [AMBER] ptraj utility case (Tue Dec 01 2009 - 06:56:52 CST)
  - Re: [AMBER] ptraj utility Neha Bharat Gajaria (Tue Dec 01 2009 - 20:13:41 CST)
[AMBER] XLEaP Error on Closing Edit Wallace Kunin (Tue Dec 01 2009 - 12:43:27 CST)
- RE: [AMBER] XLEaP Error on Closing Edit Ross Walker (Tue Dec 01 2009 - 13:02:58 CST)
[AMBER] Re: looking for parameters for DHFR substrates and inhibitors... [one more try] Sidney Elmer (Tue Dec 01 2009 - 17:34:36 CST)
- Re: [AMBER] looking for parameters for DHFR substrates and inhibitors... [one more try] FyD (Wed Dec 02 2009 - 02:19:00 CST)
[AMBER] How to get total energy of a system from QM/MM gunajyoti das (Wed Dec 02 2009 - 02:56:06 CST)
- Re: [AMBER] How to get total energy of a system from QM/MM steinbrt_at_rci.rutgers.edu (Wed Dec 02 2009 - 03:53:03 CST)
[AMBER] MMGBSA Zhongjie Liang (Wed Dec 02 2009 - 19:17:44 CST)
[AMBER] look at Amber's slides, email Sally Pias (Wed Dec 02 2009 - 23:08:47 CST)
[AMBER] Segmentation fault gurunath katagi (Thu Dec 03 2009 - 00:45:20 CST)
[AMBER] NAB example scripts in AmberTools (Amber 10) Christopher Wassman (Thu Dec 03 2009 - 03:08:37 CST)
- Re: [AMBER] NAB example scripts in AmberTools (Amber 10) case (Thu Dec 03 2009 - 07:12:27 CST)
[AMBER] binding energy of multiple ligand-receptor complex Å·ÑôµÂ·½ (Thu Dec 03 2009 - 04:51:17 CST)
- Re: [AMBER] binding energy of multiple ligand-receptor complex Oliver Kuhn (Fri Dec 04 2009 - 03:10:39 CST)
  - Re: [AMBER] binding energy of multiple ligand-receptor complex steinbrt_at_rci.rutgers.edu (Fri Dec 04 2009 - 03:47:26 CST)
    - Re: [AMBER] binding energy of multiple ligand-receptor complex Jason Swails (Fri Dec 04 2009 - 14:20:58 CST)
    - RE: [AMBER] binding energy of multiple ligand-receptor complex Å·ÑôµÂ·½ (Fri Dec 04 2009 - 15:59:21 CST)
[AMBER] QM/MM input file error mahesh kumar (Thu Dec 03 2009 - 08:05:25 CST)
- RE: [AMBER] QM/MM input file error Ross Walker (Thu Dec 03 2009 - 11:36:47 CST)
[AMBER] semiempirical copper Jacopo Sgrignani (Thu Dec 03 2009 - 08:09:57 CST)
- RE: [AMBER] semiempirical copper Ross Walker (Thu Dec 03 2009 - 11:28:45 CST)
[AMBER] Comparison of the CHARMM and AMBER parameters for alkane intra\\sa175950 (Thu Dec 03 2009 - 10:49:28 CST)
- RE: [AMBER] Comparison of the CHARMM and AMBER parameters for alkane Ross Walker (Thu Dec 03 2009 - 11:52:58 CST)
  - RE: [AMBER] Comparison of the CHARMM and AMBER parameters for alkane intra\\sa175950 (Fri Dec 04 2009 - 03:54:55 CST)
- Re: [AMBER] Comparison of the CHARMM and AMBER parameters for alkane FyD (Thu Dec 03 2009 - 13:43:10 CST)
[AMBER] AmberTools modifications for Ubuntu 9.10 peker milas (Thu Dec 03 2009 - 15:58:31 CST)
- Re: [AMBER] AmberTools modifications for Ubuntu 9.10 case (Fri Dec 04 2009 - 09:31:16 CST)
[AMBER] help with TIP4P and mpi pmemd Hashem Taha (Thu Dec 03 2009 - 16:16:22 CST)
- Re: [AMBER] help with TIP4P and mpi pmemd Robert Duke (Thu Dec 03 2009 - 16:37:14 CST)
  - [AMBER] parameter file for the sulphate ion Fenghui Fan (Thu Dec 03 2009 - 18:02:30 CST)
  - Re: [AMBER] help with TIP4P and mpi pmemd Hashem Taha (Thu Dec 03 2009 - 20:26:57 CST)
- Re: [AMBER] help with TIP4P and mpi pmemd Lizzard Man (Fri Dec 04 2009 - 16:47:08 CST)
[AMBER] Amber 10 installation: /bin/sh: ./Makelist: not found Diego Javier Alonso de Armiño (Thu Dec 03 2009 - 19:47:08 CST)
- Re: [AMBER] Amber 10 installation: /bin/sh: ./Makelist: not found Mengjuei Hsieh (Thu Dec 03 2009 - 20:52:48 CST)
- Re: [AMBER] Amber 10 installation: /bin/sh: ./Makelist: not found Jason Swails (Thu Dec 03 2009 - 20:55:09 CST)
[AMBER] sodium ions before or after solvation makes a difference Naser Alijabbari (Thu Dec 03 2009 - 23:01:13 CST)
- Re: [AMBER] sodium ions before or after solvation makes a difference Thomas Cheatham III (Fri Dec 04 2009 - 11:09:17 CST)
- Re: [AMBER] sodium ions before or after solvation makes a difference Bill Ross (Fri Dec 04 2009 - 12:23:44 CST)
[AMBER] mm_pbsa- Decomposition: bad atom type Antonija TomiÄ‡ (Fri Dec 04 2009 - 03:27:31 CST)
- Re: [AMBER] mm_pbsa- Decomposition: bad atom type Hannes Kopitz (Fri Dec 04 2009 - 04:45:10 CST)
  - Re: [AMBER] mm_pbsa- Decomposition: bad atom type Antonija TomiÄ‡ (Fri Dec 04 2009 - 04:57:59 CST)
[AMBER] ptraj usage for clustering of protein ensembles manual or tutorial Andrew Voronkov (Fri Dec 04 2009 - 03:55:05 CST)
- Re: [AMBER] ptraj usage for clustering of protein ensembles manual or tutorial Thomas Cheatham III (Fri Dec 04 2009 - 11:01:35 CST)
  - Re: [AMBER] ptraj usage for clustering of protein ensembles manual or tutorial Andrew Voronkov (Fri Dec 04 2009 - 13:09:58 CST)
- Re: [AMBER] ptraj usage for clustering of protein ensembles manual or tutorial Andrew Voronkov (Sun Dec 06 2009 - 07:39:39 CST)
[AMBER] aromatic ring getting distorted Jio M (Fri Dec 04 2009 - 04:03:49 CST)
- Re: [AMBER] aromatic ring getting distorted case (Sun Dec 06 2009 - 14:14:45 CST)
  - Re: [AMBER] aromatic ring getting distorted Jio M (Mon Dec 07 2009 - 01:04:55 CST)
[AMBER] problem with antechamber sculiujl (Fri Dec 04 2009 - 05:38:04 CST)
- Re: [AMBER] problem with antechamber Junmei Wang (Wed Dec 09 2009 - 17:24:11 CST)
[AMBER] COOH group troubling Jio M (Sun Dec 06 2009 - 07:57:06 CST)
- Re: [AMBER] COOH group troubling Jason Swails (Sun Dec 06 2009 - 09:05:07 CST)
Re: [AMBER] COOH group troubling Bill Ross (Sun Dec 06 2009 - 10:46:58 CST)
- Re: [AMBER] COOH group troubling Jio M (Sun Dec 06 2009 - 12:53:22 CST)
- Re: [AMBER] COOH group troubling Bill Ross (Sun Dec 06 2009 - 13:07:44 CST)
[AMBER] how to restart the stopped MM-GBSA job Zhongjie Liang (Sun Dec 06 2009 - 19:36:56 CST)
[AMBER] Problem of MM-PBSA Å·ÑôµÂ·½ (Sun Dec 06 2009 - 23:09:47 CST)
- Re: [AMBER] Problem of MM-PBSA Ray Luo (Mon Dec 07 2009 - 12:19:02 CST)
  - RE: [AMBER] Problem of MM-PBSA Å·ÑôµÂ·½ (Mon Dec 07 2009 - 16:30:41 CST)
    - Re: [AMBER] Problem of MM-PBSA Ray Luo (Mon Dec 07 2009 - 16:44:53 CST)
[AMBER] force field parameters Piotr Cieplak (Mon Dec 07 2009 - 01:25:03 CST)
[AMBER] phosphorus to carbon on minimization Alexander Boncheff (Mon Dec 07 2009 - 09:48:45 CST)
- Re: [AMBER] phosphorus to carbon on minimization Jason Swails (Mon Dec 07 2009 - 12:43:05 CST)
- Re: [AMBER] phosphorus to carbon on minimization FyD (Mon Dec 07 2009 - 12:56:28 CST)
[AMBER] Topology Reorder for EVB Andrea Coletta (Mon Dec 07 2009 - 09:58:50 CST)
- Re: [AMBER] Topology Reorder for EVB Jason Swails (Mon Dec 07 2009 - 12:59:23 CST)
  - Re: [AMBER] Topology Reorder for EVB Andrea Coletta (Tue Dec 08 2009 - 03:40:23 CST)
- Re: [AMBER] Topology Reorder for EVB E.M. (Mon Dec 07 2009 - 13:17:44 CST)
[AMBER] Parametrizing charges for modified DNA bases Bob Johnson (Mon Dec 07 2009 - 12:05:09 CST)
- Re: [AMBER] Parametrizing charges for modified DNA bases FyD (Mon Dec 07 2009 - 13:31:02 CST)
  - [AMBER] Re: EEL = ************* Taufik Al-Sarraj (Tue Dec 08 2009 - 12:34:35 CST)
[AMBER] question about failures peker milas (Mon Dec 07 2009 - 21:37:40 CST)
- Re: [AMBER] question about failures Jason Swails (Mon Dec 07 2009 - 22:51:28 CST)
  - Re: [AMBER] question about failures peker milas (Mon Dec 07 2009 - 23:31:06 CST)
    - Re: [AMBER] question about failures Jason Swails (Tue Dec 08 2009 - 00:00:00 CST)
    - Re: [AMBER] question about failures peker milas (Tue Dec 08 2009 - 00:25:10 CST)
[AMBER] myristate to palmitate transformation Anthony Pemberton (Tue Dec 08 2009 - 10:24:59 CST)
[AMBER] Custom RNA modeling Wallace Kunin (Tue Dec 08 2009 - 14:27:55 CST)
- Re: [AMBER] Custom RNA modeling Ilyas Yildirim (Tue Dec 08 2009 - 16:01:42 CST)
  - Re: [AMBER] Custom RNA modeling Wallace Kunin (Wed Dec 09 2009 - 10:10:44 CST)
Re: [AMBER] ptraj image Bill Ross (Tue Dec 08 2009 - 16:08:42 CST)
- Re: [AMBER] ptraj image Taufik Al-Sarraj (Tue Dec 08 2009 - 17:54:46 CST)
  - Re: [AMBER] ptraj image Daniel Roe (Wed Dec 09 2009 - 10:21:18 CST)
[AMBER] Nmode "not running properly" problem in MM_PBSA Du Yun (Tue Dec 08 2009 - 19:56:48 CST)
- Re: [AMBER] Nmode "not running properly" problem in MM_PBSA case (Sun Dec 13 2009 - 09:06:36 CST)
[AMBER] PIMD test stalling peker milas (Tue Dec 08 2009 - 20:23:45 CST)
- [AMBER] Re: PIMD test stalling peker milas (Tue Dec 08 2009 - 21:11:44 CST)
[AMBER] how to add desired number of water balaji nagarajan (Tue Dec 08 2009 - 21:18:49 CST)
- Re: [AMBER] how to add desired number of water Simon Becker (Wed Dec 09 2009 - 10:09:51 CST)
[AMBER] ptraj image Neha Bharat Gajaria (Wed Dec 09 2009 - 00:13:36 CST)
- Re: [AMBER] ptraj image Bill Ross (Tue Dec 08 2009 - 18:29:03 CST)
- Re: [AMBER] ptraj image Thomas Cheatham (Wed Dec 09 2009 - 07:41:54 CST)
[AMBER] Re: ATP/GTP parameters FyD (Wed Dec 09 2009 - 00:51:03 CST)
[AMBER] Re: COOH troubling Jio M (Wed Dec 09 2009 - 06:16:17 CST)
- Re: [AMBER] Re: COOH troubling case (Wed Dec 09 2009 - 07:40:10 CST)
  - Re: [AMBER] Re: COOH troubling Jio M (Wed Dec 09 2009 - 09:01:30 CST)
- Re: [AMBER] Re: COOH troubling Junmei Wang (Wed Dec 09 2009 - 17:17:12 CST)
  - Re: [AMBER] Re: COOH troubling Dean Cuebas (Wed Dec 09 2009 - 18:00:40 CST)
- Re: [AMBER] Re: COOH troubling Jio M (Sat Dec 12 2009 - 00:27:25 CST)
[AMBER] Re: COOH group trouble Jio M (Wed Dec 09 2009 - 10:38:09 CST)
Re: [AMBER] how to add desired number of water Bill Ross (Wed Dec 09 2009 - 11:46:59 CST)
[AMBER] pressure tensor components Silvia Carlotto (Thu Dec 10 2009 - 07:12:51 CST)
- Re: [AMBER] pressure tensor components case (Sun Dec 13 2009 - 09:10:02 CST)
[AMBER] MMPBSA on a selected region ERIK.LAURINI_at_phd.units.it (Thu Dec 10 2009 - 12:20:19 CST)
- Re: [AMBER] MMPBSA on a selected region Jason Swails (Thu Dec 10 2009 - 13:15:58 CST)
[AMBER] why is the ff03 force field in Amber8 and Amber10 different for Ala2 dipeptide Dongshan Wei (Thu Dec 10 2009 - 17:40:19 CST)
- Re: [AMBER] why is the ff03 force field in Amber8 and Amber10 different for Ala2 dipeptide Carlos Simmerling (Thu Dec 10 2009 - 17:52:40 CST)
- RE: [AMBER] why is the ff03 force field in Amber8 and Amber10 different for Ala2 dipeptide Ross Walker (Thu Dec 10 2009 - 18:02:16 CST)
  - Re: [AMBER] why is the ff03 force field in Amber8 and Amber10 different for Ala2 dipeptide Dongshan Wei (Thu Dec 10 2009 - 18:14:12 CST)
[AMBER] QM/MM minimization Hashem Taha (Fri Dec 11 2009 - 12:24:25 CST)
- Re: [AMBER] QM/MM minimization Pansy Patel (Thu Sep 10 2009 - 09:09:48 CDT)
- RE: [AMBER] QM/MM minimization Ross Walker (Fri Dec 11 2009 - 21:39:55 CST)
[AMBER] amber10 pmemd fail Aragorn Steiger (Fri Dec 11 2009 - 14:35:49 CST)
- Re: [AMBER] amber10 pmemd fail Robert Duke (Fri Dec 11 2009 - 15:40:31 CST)
- RE: [AMBER] amber10 pmemd fail Ross Walker (Fri Dec 11 2009 - 21:43:53 CST)
FW: Solvent/solute ratio? Re: [AMBER] how to add desired number of water Hopkins, Robert (Fri Dec 11 2009 - 16:05:51 CST)
- Re: FW: Solvent/solute ratio? Re: [AMBER] how to add desired number of water Bill Ross (Fri Dec 11 2009 - 16:19:57 CST)
  - RE: FW: Solvent/solute ratio? Re: [AMBER] how to add desired numberof water Richard Owczarzy (Fri Dec 11 2009 - 18:19:31 CST)
    - RE: FW: Solvent/solute ratio? Re: [AMBER] how to add desired numberof water Bill Ross (Fri Dec 11 2009 - 18:57:41 CST)
  - RE: FW: Solvent/solute ratio? Re: [AMBER] how to add desired number of water Ross Walker (Fri Dec 11 2009 - 21:47:19 CST)
Re: FW: Solvent/solute ratio? Re: [AMBER] how to add desired numberof water Hopkins, Robert (Fri Dec 11 2009 - 16:24:02 CST)
- Re: Solvent/solute ratio? Re: [AMBER] how to add desired numberof water Dean Cuebas (Mon Dec 14 2009 - 20:40:25 CST)
RE: [Possible Spam: 10%] RE: FW: Solvent/solute ratio? Re: [AMBER] how to add desirednumberof water Hopkins, Robert (Sat Dec 12 2009 - 18:29:04 CST)
[AMBER] amber@ambermd.org shumao_at_cqut.edu.cn (Sun Dec 13 2009 - 21:01:18 CST)
[AMBER] How to run LEaP in a shell file? SongLin (Mon Dec 14 2009 - 01:10:00 CST)
- Re: [AMBER] How to run LEaP in a shell file? case (Mon Dec 14 2009 - 06:44:29 CST)
  - Re: [AMBER] How to run LEaP in a shell file? SongLin (Mon Dec 14 2009 - 07:45:03 CST)
[AMBER] Different simulation times for similar systems Oliver Kuhn (Mon Dec 14 2009 - 06:31:50 CST)
- Re: [AMBER] Different simulation times for similar systems Carlos Simmerling (Mon Dec 14 2009 - 12:11:56 CST)
[AMBER] how can i include ANP residue Bradley Dickson (Mon Dec 14 2009 - 09:07:50 CST)
- Re: [AMBER] how can i include ANP residue FyD (Mon Dec 14 2009 - 14:29:42 CST)
  - Re: [AMBER] how can i include ANP residue Bradley Dickson (Mon Dec 14 2009 - 16:00:32 CST)
    - Re: [AMBER] how can i include ANP residue David Watson (Mon Dec 14 2009 - 16:44:30 CST)
[AMBER] Installation on MacOSX Freedman, Tanya (Mon Dec 14 2009 - 12:59:06 CST)
- Re: [AMBER] Installation on MacOSX David Watson (Mon Dec 14 2009 - 14:01:52 CST)
  - Re: [AMBER] Installation on MacOSX Alan (Tue Dec 15 2009 - 04:26:48 CST)
[AMBER] comparing coordinates from restart file and ptraj outputs Sidney Elmer (Mon Dec 14 2009 - 19:23:50 CST)
- Re: [AMBER] comparing coordinates from restart file and ptraj outputs Jason Swails (Mon Dec 14 2009 - 19:53:39 CST)
- Re: [AMBER] comparing coordinates from restart file and ptraj outputs case (Mon Dec 14 2009 - 21:28:32 CST)
  - Re: [AMBER] comparing coordinates from restart file and ptraj outputs Sidney Elmer (Tue Dec 15 2009 - 02:21:35 CST)
[AMBER] Number of Cycles s. Bill (Tue Dec 15 2009 - 02:31:21 CST)
- Re: [AMBER] Number of Cycles Jason Swails (Tue Dec 15 2009 - 06:10:02 CST)
  - Re: [AMBER] Number of Cycles Robert Duke (Tue Dec 15 2009 - 07:16:51 CST)
- Re: [AMBER] Number of Cycles Jason Swails (Tue Dec 15 2009 - 07:32:31 CST)
  - Re: [AMBER] Number of Cycles Jason Swails (Tue Dec 15 2009 - 07:34:29 CST)
- Re: [AMBER] Number of Cycles Bill Ross (Tue Dec 15 2009 - 11:53:24 CST)
[AMBER] addles - neb error balaji nagarajan (Tue Dec 15 2009 - 08:38:53 CST)
- RE: [AMBER] addles - neb error Ross Walker (Tue Dec 15 2009 - 10:45:19 CST)
  - RE: [AMBER] addles - neb error balaji nagarajan (Tue Dec 15 2009 - 21:26:51 CST)
    - Re: [AMBER] addles - neb error case (Wed Dec 16 2009 - 15:01:20 CST)
    - RE: [AMBER] addles - neb error balaji nagarajan (Wed Dec 16 2009 - 21:20:22 CST)
[AMBER] non standard residue and bond command Neha Bharat Gajaria (Wed Dec 16 2009 - 03:50:02 CST)
- Re: [AMBER] non standard residue and bond command case (Wed Dec 16 2009 - 15:06:34 CST)
- Re: [AMBER] non standard residue and bond command Bill Ross (Wed Dec 16 2009 - 15:20:08 CST)
[AMBER] chemical shifts: nter and cter Eliana Asciutto (Wed Dec 16 2009 - 13:55:14 CST)
- Re: [AMBER] chemical shifts: nter and cter case (Wed Dec 16 2009 - 14:52:11 CST)
[AMBER] NAMD dcd files in ptraj Ganesh Kamath (Wed Dec 16 2009 - 15:04:25 CST)
[AMBER] Parameters for HYP and CGU Rilei Yu (Wed Dec 16 2009 - 21:17:40 CST)
- Re: [AMBER] Parameters for HYP and CGU Adrian Roitberg (Wed Dec 16 2009 - 21:27:25 CST)
  - Re: [AMBER] Parameters for HYP and CGU Rilei Yu (Wed Dec 16 2009 - 23:58:26 CST)
- Re: [AMBER] Parameters for HYP and CGU Jason Swails (Wed Dec 16 2009 - 21:58:02 CST)
  - Re: [AMBER] Parameters for HYP and CGU Rilei Yu (Wed Dec 16 2009 - 23:57:13 CST)
- Re: [AMBER] Parameters for HYP and CGU FyD (Thu Dec 17 2009 - 02:46:55 CST)
  - Re: [AMBER] Parameters for HYP and CGU Alessandro Contini (Thu Dec 17 2009 - 03:11:44 CST)
  - [AMBER] branched aminoacids Alessandro Contini (Thu Dec 17 2009 - 03:14:34 CST)
    - Re: [AMBER] branched aminoacids FyD (Thu Dec 17 2009 - 03:49:16 CST)
    - Re: [AMBER] branched aminoacids Alessandro Contini (Thu Dec 17 2009 - 05:22:56 CST)
[AMBER] C1, C2 & C3 carbon types in generalized Born implementation igb=5 Nils Jan Daniel Drechsel (Thu Dec 17 2009 - 03:52:59 CST)
- Re: [AMBER] C1, C2 & C3 carbon types in generalized Born implementation igb=5 case (Thu Dec 17 2009 - 07:03:27 CST)
  - Re: [AMBER] C1, C2 & C3 carbon types in generalized Born implementation igb=5 Nils Jan Daniel Drechsel (Fri Dec 18 2009 - 04:37:53 CST)
[AMBER] what the value of "Br" bondi radii, and how to modify "fillratio" error message. B (Thu Dec 17 2009 - 03:59:29 CST)
[AMBER] MM_PBSA Problem (no radius for ion) s. Bill (Thu Dec 17 2009 - 13:39:49 CST)
- Re: [AMBER] MM_PBSA Problem (no radius for ion) Scott Brozell (Thu Dec 17 2009 - 21:07:21 CST)
  - Re: [AMBER] MM_PBSA Problem (no radius for ion) s. Bill (Fri Dec 18 2009 - 09:33:57 CST)
[AMBER] Compatibility of ONIOM and Amber vaibhav dixit (Fri Dec 18 2009 - 00:30:32 CST)
[AMBER] Inorganic Phosphate Parameters Cihan Aydin (Fri Dec 18 2009 - 14:19:21 CST)
- Re: [AMBER] Inorganic Phosphate Parameters. . Don.Bashford_at_stjude.org (Fri Dec 18 2009 - 16:12:58 CST)
  - Re: [AMBER] Inorganic Phosphate Parameters. . Jason Swails (Fri Dec 18 2009 - 16:54:39 CST)
  - Re: [AMBER] Inorganic Phosphate Parameters. . case (Sat Dec 19 2009 - 11:39:28 CST)
[AMBER] antechamber bond type error Mark M Huntress (Fri Dec 18 2009 - 16:26:57 CST)
- Re: [AMBER] antechamber bond type error case (Sat Dec 19 2009 - 11:33:40 CST)
[AMBER] note on Antechamber error Mark M Huntress (Fri Dec 18 2009 - 16:27:50 CST)
[AMBER] SQM and AMBER Jio M (Sat Dec 19 2009 - 00:36:05 CST)
[AMBER] Non-Standard Atoms Jack Shultz (Sat Dec 19 2009 - 19:56:28 CST)
- Re: [AMBER] Non-Standard Atoms Jason Swails (Sat Dec 19 2009 - 20:54:20 CST)
- Re: [AMBER] Non-Standard Atoms case (Sun Dec 20 2009 - 13:02:46 CST)
  - Re: [AMBER] Non-Standard Atoms Jack Shultz (Sun Dec 20 2009 - 18:40:26 CST)
[AMBER] hi ashish pandey (Mon Dec 21 2009 - 00:45:40 CST)
- Re: [AMBER] hi David Watson (Mon Dec 21 2009 - 03:09:53 CST)
[AMBER] Sander crash, corrupt rst file... Waqas Nasir (Mon Dec 21 2009 - 05:44:42 CST)
[AMBER] (No reply) Compatibility of ONIOM and Amber vaibhav dixit (Mon Dec 21 2009 - 07:58:03 CST)
[AMBER] Release of AmberTools, version 1.3 David A. Case (Mon Dec 21 2009 - 08:33:20 CST)
[AMBER] Gaff compatible with ff899.SB Pol Boudard (Mon Dec 21 2009 - 09:03:25 CST)
- Re: [AMBER] Gaff compatible with ff899.SB Carlos Simmerling (Mon Dec 21 2009 - 09:32:40 CST)
[AMBER] MM PBSA stats Peter Jones (Mon Dec 21 2009 - 23:57:51 CST)
[AMBER] PQR file - HELP PLEASE s. Bill (Tue Dec 22 2009 - 06:57:48 CST)
- Re: [AMBER] PQR file - HELP PLEASE Jason Swails (Tue Dec 22 2009 - 11:21:41 CST)
  - Re: [AMBER] PQR file - HELP PLEASE s. Bill (Tue Dec 22 2009 - 15:27:48 CST)
[AMBER] MMGBSA error Zhongjie Liang (Tue Dec 22 2009 - 07:04:09 CST)
- Re: [AMBER] MMGBSA error Carlos Simmerling (Tue Dec 22 2009 - 07:05:41 CST)
  - ´ð¸´: [AMBER] MMGBSA error Zhongjie Liang (Wed Dec 23 2009 - 07:12:07 CST)
[AMBER] sqm x mopac in AmberTools 1.3 Alan (Tue Dec 22 2009 - 09:02:22 CST)
- Re: [AMBER] sqm x mopac in AmberTools 1.3 David Watson (Tue Dec 22 2009 - 09:20:37 CST)
  - Re: [AMBER] sqm x mopac in AmberTools 1.3 David Watson (Tue Dec 22 2009 - 09:58:56 CST)
  - Re: [AMBER] sqm x mopac in AmberTools 1.3 David A. Case (Tue Dec 22 2009 - 21:53:20 CST)
- Re: [AMBER] sqm x mopac in AmberTools 1.3 David A. Case (Tue Dec 22 2009 - 21:50:35 CST)
  - Re: [AMBER] sqm x mopac in AmberTools 1.3 Alan (Tue Dec 29 2009 - 12:49:26 CST)
    - Re: [AMBER] sqm x mopac in AmberTools 1.3 case (Tue Dec 29 2009 - 13:49:26 CST)
    - Re: [AMBER] sqm x mopac in AmberTools 1.3 Alan (Tue Dec 29 2009 - 13:52:44 CST)
[AMBER] Van der Waals and electrostatic Forces Frank X. Vázquez (Tue Dec 22 2009 - 11:42:33 CST)
- Re: [AMBER] Van der Waals and electrostatic Forces David A. Case (Wed Dec 23 2009 - 20:56:50 CST)
[AMBER] HOW TO OPTIMISE INDI-DIELC_MM VALUE for MM_PBSA calculation ? Marek Maly (Tue Dec 22 2009 - 12:49:42 CST)
[AMBER] pupil and amber davide branduardi (Tue Dec 22 2009 - 14:29:37 CST)
- Re: [AMBER] pupil and amber Ben Roberts (Tue Dec 22 2009 - 20:59:04 CST)
[AMBER] atom type shamoon siddiqui (Tue Dec 22 2009 - 23:31:42 CST)
- Re: [AMBER] atom type FyD (Wed Dec 23 2009 - 07:00:39 CST)
[AMBER] AmberTools-1.3 not compiling on MacOsX Cesar Millan (Wed Dec 23 2009 - 00:37:37 CST)
- Re: [AMBER] AmberTools-1.3 not compiling on MacOsX David Watson (Wed Dec 23 2009 - 00:59:09 CST)
  - Re: [AMBER] AmberTools-1.3 not compiling on MacOsX Mengjuei Hsieh (Wed Dec 23 2009 - 03:12:19 CST)
    - Re: [AMBER] AmberTools-1.3 not compiling on MacOsX Mengjuei Hsieh (Wed Dec 23 2009 - 04:05:48 CST)
    - Re: [AMBER] AmberTools-1.3 not compiling on MacOsX Jason Swails (Wed Dec 23 2009 - 05:38:08 CST)
[AMBER] typo in AmberTools.pdf (release 1.3) Alan (Wed Dec 23 2009 - 03:51:01 CST)
- Re: [AMBER] typo in AmberTools.pdf (release 1.3) David A. Case (Wed Dec 23 2009 - 08:26:51 CST)
[AMBER] using sqm from AmberTools 1.3 Alan (Wed Dec 23 2009 - 04:35:33 CST)
- Re: [AMBER] using sqm from AmberTools 1.3 David A. Case (Wed Dec 23 2009 - 08:16:04 CST)
  - Re: [AMBER] using sqm from AmberTools 1.3 David A. Case (Wed Dec 23 2009 - 08:26:36 CST)
- RE: [AMBER] using sqm from AmberTools 1.3 Ross Walker (Thu Dec 24 2009 - 17:17:47 CST)
  - Re: [AMBER] using sqm from AmberTools 1.3 Alan (Tue Dec 29 2009 - 11:35:06 CST)
[AMBER] NEB-error balaji nagarajan (Wed Dec 23 2009 - 10:04:46 CST)
- Re: [AMBER] NEB-error Carlos Simmerling (Wed Dec 23 2009 - 10:12:01 CST)
  - [AMBER] How to put another 10 ligands into the simulation system? Chih-Ying Lin (Wed Dec 23 2009 - 10:18:47 CST)
    - Re: [AMBER] How to put another 10 ligands into the simulation system? David A. Case (Thu Dec 24 2009 - 11:17:11 CST)
  - Re: Re: [AMBER] NEB-error xmzpzengs (Wed Dec 23 2009 - 10:44:36 CST)
[AMBER] CHARMM psf file to Amber prmtop file Sarvin Moghaddam (Wed Dec 23 2009 - 10:20:30 CST)
- Re: [AMBER] CHARMM psf file to Amber prmtop file xmzpzengs (Wed Dec 23 2009 - 10:40:28 CST)
- Re: [AMBER] CHARMM psf file to Amber prmtop file Jason Swails (Wed Dec 23 2009 - 14:32:11 CST)
- Re: [AMBER] CHARMM psf file to Amber prmtop file David A. Case (Wed Dec 23 2009 - 20:39:24 CST)
- RE: [AMBER] CHARMM psf file to Amber prmtop file Ross Walker (Thu Dec 24 2009 - 17:11:36 CST)
[AMBER] iron in prepi file generation for heme Donald Keidel (Wed Dec 23 2009 - 16:27:10 CST)
- Re: [AMBER] iron in prepi file generation for heme David A. Case (Thu Dec 24 2009 - 11:27:07 CST)
[AMBER] Adding single distance restraint Adler, Marc (Wed Dec 23 2009 - 20:00:35 CST)
- Re: [AMBER] Adding single distance restraint Jason Swails (Wed Dec 23 2009 - 21:11:48 CST)
[AMBER] SQM and AMBER :again Jio M (Wed Dec 23 2009 - 23:18:37 CST)
[AMBER] OE and CG types Jio M (Thu Dec 24 2009 - 03:26:43 CST)
- Re: [AMBER] OE and CG types Jason Swails (Thu Dec 24 2009 - 06:46:35 CST)
  - Re: [AMBER] OE and CG types Jio M (Thu Dec 24 2009 - 09:18:31 CST)
[AMBER] implicit solvent MD with fixed residues Hakan Gunaydin (Thu Dec 24 2009 - 17:43:13 CST)
- Re: [AMBER] implicit solvent MD with fixed residues David A. Case (Fri Dec 25 2009 - 14:22:31 CST)
[AMBER] RE: Amber question Ross Walker (Thu Dec 24 2009 - 17:44:54 CST)
[AMBER] a problem in building oligosaccharides using LEaP Song Lin (Thu Dec 24 2009 - 20:12:10 CST)
[AMBER] MMGBSA error Zhongjie Liang (Fri Dec 25 2009 - 00:59:16 CST)
- Re: [AMBER] MMGBSA error Jason Swails (Fri Dec 25 2009 - 07:28:15 CST)
  - Re: [AMBER] MMGBSA error David A. Case (Fri Dec 25 2009 - 16:17:26 CST)
    - ´ð¸´: [AMBER] MMGBSA error Zhongjie Liang (Fri Dec 25 2009 - 22:30:00 CST)
[AMBER] FW: how to change velocities balaji nagarajan (Fri Dec 25 2009 - 04:23:57 CST)
- Re: [AMBER] FW: how to change velocities Carlos Simmerling (Fri Dec 25 2009 - 06:13:44 CST)
  - RE: [AMBER] FW: how to change velocities balaji nagarajan (Sat Dec 26 2009 - 00:02:58 CST)
    - Re: [AMBER] FW: how to change velocities Carlos Simmerling (Sat Dec 26 2009 - 07:26:17 CST)
[AMBER] a question about ptraj qiaoyan (Fri Dec 25 2009 - 07:58:44 CST)
[AMBER] PQR files s. Bill (Fri Dec 25 2009 - 08:38:36 CST)
- Re: [AMBER] PQR files Jason Swails (Fri Dec 25 2009 - 10:57:51 CST)
  - Re: [AMBER] PQR files s. Bill (Fri Dec 25 2009 - 12:27:22 CST)
[AMBER] heating system in NEB balaji nagarajan (Sat Dec 26 2009 - 05:29:35 CST)
[AMBER] reg.changing velocity balaji nagarajan (Sat Dec 26 2009 - 12:47:10 CST)
- Re: [AMBER] reg.changing velocity David A. Case (Sat Dec 26 2009 - 21:01:18 CST)
[AMBER] neb error while heating balaji nagarajan (Sat Dec 26 2009 - 21:09:00 CST)
- Re: [AMBER] neb error while heating Carlos Simmerling (Mon Dec 28 2009 - 11:34:56 CST)
[AMBER] .rst file error ZhaoLei (Sun Dec 27 2009 - 08:46:37 CST)
- RE: [AMBER] .rst file error ZhaoLei (Sun Dec 27 2009 - 20:37:57 CST)
  - RE: [AMBER] .rst file error ZhaoLei (Sun Dec 27 2009 - 21:09:24 CST)
- Re: [AMBER] .rst file error Jia Xu (Mon Dec 28 2009 - 02:00:57 CST)
  - RE: [AMBER] .rst file error ZhaoLei (Mon Dec 28 2009 - 04:36:17 CST)
[AMBER] coarse grained Francesco Pietra (Sun Dec 27 2009 - 14:36:02 CST)
[AMBER] ERROR: Could not read coords from {filename} Paul Brandt (Sun Dec 27 2009 - 22:14:50 CST)
- Re: [AMBER] ERROR: Could not read coords from {filename} case (Mon Dec 28 2009 - 07:00:34 CST)
  - RE: [AMBER] ERROR: Could not read coords from {filename} ZhaoLei (Mon Dec 28 2009 - 08:12:54 CST)
  - RE: [AMBER] ERROR: Could not read coords from {filename} Paul Brandt (Tue Dec 29 2009 - 03:46:55 CST)
[AMBER] problem in installing amber tools on Mac OSX 10.6 Chun-Wei Pao (Mon Dec 28 2009 - 01:54:26 CST)
- Re: [AMBER] problem in installing amber tools on Mac OSX 10.6 David Watson (Mon Dec 28 2009 - 07:06:30 CST)
- Re: [AMBER] problem in installing amber tools on Mac OSX 10.6 case (Mon Dec 28 2009 - 07:07:48 CST)
[AMBER] About APBS radiopt Youn Kyeung Lee (Mon Dec 28 2009 - 04:12:07 CST)
- Re: [AMBER] About APBS radiopt Robert Konecny (Mon Dec 28 2009 - 09:43:18 CST)
[AMBER] NEB-NAN error balaji nagarajan (Mon Dec 28 2009 - 09:16:43 CST)
[AMBER] mpirun error Vijay Manickam Achari (Mon Dec 28 2009 - 21:00:11 CST)
[AMBER] nab installation Lixia Jin Day (Tue Dec 29 2009 - 11:32:37 CST)
- Re: [AMBER] nab installation case (Tue Dec 29 2009 - 13:26:35 CST)
[AMBER] can I install amber11 on a windowsPC under cygwin? Lixia Jin Day (Tue Dec 29 2009 - 12:06:30 CST)
- Re: [AMBER] can I install amber11 on a windowsPC under cygwin? Jason Swails (Tue Dec 29 2009 - 13:42:34 CST)
- Re: [AMBER] can I install amber11 on a windowsPC under cygwin? Mengjuei Hsieh (Tue Dec 29 2009 - 13:44:06 CST)
- Re: [AMBER] can I install amber11 on a windowsPC under cygwin? case (Tue Dec 29 2009 - 13:44:18 CST)
- Re: [AMBER] can I install amber11 on a windowsPC under cygwin? Bill Ross (Tue Dec 29 2009 - 15:05:07 CST)
  - Re: [AMBER] can I install amber11 on a windowsPC under cygwin? Jason Swails (Tue Dec 29 2009 - 17:08:38 CST)
    - Re: [AMBER] can I install amber11 on a windowsPC under cygwin? case (Tue Dec 29 2009 - 17:36:46 CST)
[AMBER] sleap in AmberTools 1.3 is not working anymore for me Alan (Tue Dec 29 2009 - 14:27:57 CST)
- Re: [AMBER] sleap in AmberTools 1.3 is not working anymore for me David Watson (Tue Dec 29 2009 - 15:02:05 CST)
  - Re: [AMBER] sleap in AmberTools 1.3 is not working anymore for me Alan (Tue Dec 29 2009 - 15:47:52 CST)
- Re: [AMBER] sleap in AmberTools 1.3 is not working anymore for me case (Tue Dec 29 2009 - 21:40:26 CST)
[AMBER] Tests to check for proper MMPBSA.py installation RANAJIT SHINDE (Wed Dec 30 2009 - 06:15:48 CST)
- Re: [AMBER] Tests to check for proper MMPBSA.py installation case (Wed Dec 30 2009 - 08:23:57 CST)
[AMBER] exchange attempt in REMD zgong.hust (Wed Dec 30 2009 - 20:34:21 CST)
- Re: [AMBER] exchange attempt in REMD Carlos Simmerling (Wed Dec 30 2009 - 21:09:02 CST)
  - Re: Re: [AMBER] exchange attempt in REMD zgong.hust (Wed Dec 30 2009 - 22:22:54 CST)
    - Re: Re: [AMBER] exchange attempt in REMD Carlos Simmerling (Thu Dec 31 2009 - 09:50:24 CST)
[AMBER] Zinc parameters? xuemeiwang1103 (Wed Dec 30 2009 - 21:37:21 CST)
- Re: [AMBER] Zinc parameters? Ray Luo, Ph.D. (Thu Dec 31 2009 - 20:11:45 CST)
- Re: [AMBER] Zinc parameters? vhakkim boy (Thu Dec 31 2009 - 22:56:50 CST)

Last message date: Thu Dec 31 2009 - 22:57:46 CST
Archived on: Thu Dec 31 2009 - 22:58:32 CST

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